UDP-N-acetylglucosamine: galactose-beta1,3-N-acetylgalactosamine-alpha-R / (GlcNAc to GalNAc) beta1,6-N-acetylglucosaminyltransferase, C2GnT3

ABSTRACT

A novel gene defining a novel human UDP-GlcNAc: Galβ1-3GalNAcα β1,6GlcNAc-transferase, termed C2GnT3, with unique enzymatic properties is disclosed. The enzymatic activity of C2GnT3 is shown to be distinct from that of previously identified enzymes of this gene family. The invention discloses isolated DNA molecules and DNA constructs encoding C2GnT3 and derivatives thereof by way of amino acid deletion, substitution or insertion exhibiting C2GnT3 activity, as well as cloning and expression vectors including such DNA, cells transfected with the vectors, and recombinant methods for providing C2GnT3. The enzyme C2GnT3 and C2GnT3 -active derivatives thereof are disclosed, in particular soluble derivatives comprising the catalytically active domain of C2GnT3. Further, the invention discloses methods of obtaining 1,6-N-acetylglucosaminyl glycosylated saccharides, glycopeptides or glycoproteins by use of an enzymically active C2GnT3 protein or fusion protein thereof or by using cells stably transfected with a vector including DNA encoding an enzymatically active C2GnT3 protein as an expression system for recombinant production of such glycopeptides or glycoproteins. Methods are disclosed for the identification of agents with the ability to inhibit or stimulate the biological activity of C2GnT3. Furthermore, methods of using C2GnT3 in the structure-based design of inhibitors or stimulators thereof are also disclosed in the invention. Also a method for the identification of DNA sequence variations in the C2GnT3 gene by isolating DNA from a patient, amplifying C2GnT3-coding exons by PCR, and detecting the presence of DNA sequence variation, are disclosed.

[0001] This application is a divisional of U.S. Ser. No. 09/645,192,filed Aug. 24, 2000, which claims priority to U.S. Ser. No. 60/150,488,filed Aug. 24, 1999. Each of these prior applications is incorporated byreference in its entirety.

TECHNICAL FIELD

[0002] The present invention relates generally to the biosynthesis ofglycans found as free oligosaccharides or covalently bound to proteinsand glycolipids. In particular, this invention relates to a family ofnucleic acids encoding UDP-N-acetylglucosamine:N-acetylgalactosamine-β1,6-N-acetylglucosaminyltransferases(Core-β1,6-N-acetylglucosaminyltransferases), which addN-acetylglucosamine to the hydroxy group at C6 of2-acetamido-2-deoxy-D-galactosamine (GalNAc) in O-glycans of the core 1and the core 3 type thereby forming the core 2 and core 4 types.Previously two members of this family have been identified anddesignated C2GnT1 and C2GnT2.

[0003] This invention is more particularly related to a gene encoding athird member of this family of O-glycanβ1,6-N-acetylglucosaminyltransferases, termed C2GnT3, probes to the DNAencoding C2GnT3, DNA constructs comprising DNA encoding C2GnT3,recombinant plasmids and recombinant methods for producing C2GnT3,recombinant methods for stably transforming or transfecting cells forexpression of C2GnT3, methods for identification of agents with theability to inhibit or stimulate C2GnT3 biological activity, and methodsfor identification of DNA polymorphism in patients. In the U.S.Provisional Patent Application No. 60/150,488 filed on Aug. 24, 1999,from which the present application claims priority, this novel Core 2β6GlcNAc-transferase isoform was identified and designated C2GnTII. Thedesignation C2GnTII has here been replaced by the designation C2GnT3 inaccordance with its scientific publication (14).

BACKGROUND OF THE INVENTION

[0004] O-linked protein glycosylation involves an initiation stage inwhich a family of N-acetylgalactosaminyltransferases catalyzes theaddition of N-acetylgalactosamine to Serine or Threonine residues (1).Further assembly of O-glycan chains involves several sucessive oralternative biosynthetic reactions: i) formation of simple mucin-typecore 1 structures by UDP-Gal: GalNAcα-R β1,3Gal-transferase activity;ii) conversion of core 1 to complex-type core 2 structures byUDP-GlcNAc: Galα1-3GalNAcα-R β1,6GlcNAc-transferase activities; iii)direct formation of complex mucin-type core 3 by UDP-GlcNAc: GalNAcαβ1,3GlcNAc-transferase activities; and iv) conversion of core 3 to core4 by UDP-GlcNAc: GlcNAcβ1-3GalNAcα-R β1,6GlcNAc-transferase activity.The formation of β1,6GlcNAc branches (reactions ii and iv) may beconsidered a key controlling event of O-linked protein glycosylationleading to structures produced upon differentiation and malignanttransformation (2-6). For example, increased formation of GlcNAc1-6GalNAc branching in O-glycans has been demonstrated during T-cellactivation, during the development of leukemia, and forimmunodeficiencies like Wiskott-Aldrich syndrome and AIDS (7; 8). Core 2branching may play a role in tumor progression and metastasis (9). Incontrast, many carcinomas show changes from complex O-glycans found innormal cell types to immaturely processed simple mucin-type O-glycanssuch as T (Thomsen-Friedenreich antigen; Galβ1-3GalNAcα1-R), Tn(GalNAcα1-R), and sialosyl-Tn (NeuAcα2-6GalNAcα1-R) (10). The molecularbasis for this has been extensively studied in breast cancer, where itwas shown that specific downregulation of a core 2 β6GlcNAc-transferasewas responsible for the observed lack of complex type O-glycans on themucin MUCl (6). O-glycan core assembly may therefore be controlled byinverse changes in the expression level ofCore-β1,6-N-acetylglucosaminyltransferases and the sialyltransferasesforming sialyl-T and sialyl-Tn.

[0005] Interestingly, the metastatic potential of tumors has beencorrelated with increased expression of core 2 β6GlcNAc-transferaseactivity (5). The increase in core 2 β6GlcNAc-transferase activity wasassociated with increased levels of poly N-acetyllactosamine chainscarrying sialyl-Le^(X), which may contribute to tumor metastasis byaltering selectin-mediated adhesion (4; 11). The control of O-glycancore assembly is regulated by the expression of key enzyme activities;however, epigenetic factors including posttranslational modification,topology, or competition for substrates may also play a role in thisprocess (11).

[0006] Changes in surface carbohydrates of T-cells have been identifiedduring development and activation. O-glycan branches of the core 2 typeare restricted to immature thymocytes of the thymal cortex but are nolonger exposed on the surface of mature medullary thymocytes (17). Core2 structures on T-cell surface proteins are ligands for the S-typelectin galectin-1, which participates in thymocyte —thymic epitheliainteraction (18). The elimination of Core 2 structures from thethymocyte cell surface was found to be essential for controlledapoptosis mediated by galectin-1(19).

[0007] Core 2 β6GlcNAc-transferase activity is carried out by more thanone enzyme isoform. The first Core 2 β6GlcNAc-transferase isoform wasinitially identified as a critical enzyme in blood cell development anddifferentiation and designated leukocyte form or L-Form (C2GnT-L)(12).The gene encoding C2GnT-L has been cloned by expression cloning from acDNA library of the human promyelocytic leukemia cell line HL-60 (13).This gene has now been renamed as C2GnT1 (14). Using the C2GnT1 sequenceas a probe for BLAST analysis of the human expressed sequence tagdatabase, a homologous gene encoding a second Core 2β6GlcNAc-transferase isoform has been identified and designated C2/4GnT(15) and C2GnT-M (16). This gene has now been renamed as C2GnT2 (14).

[0008] C2GnT1 was predicted to control synthesis of core 2 selectinligands in leukocytes and lymphoid tissues, however, mice deficient inC2GnT1 exhibited only partial reduction in selectin ligand productionand no significant changes in lymphocyte homing properties (Ellies, L.G., et al. 1998, Immunity 9: 881-890). One possible explanation forthese results would be the expression of additional Core 2β6GlcNAc-transferases. C2GnT2 does not appear to be a candidate, as itsexpression pattern is restricted to mucous secreting organs (15, 16).

[0009] Consequently, there exists a need in the art for detecting as yetunidentified UDP-N-acetylglucosamine:Galactose-β1,3-N-acetylgalactosamine-α-R (GlcNAc to GalNAc) β1-6N-acetylglucosaminyltransferases and identifying the primary structuresof the genes encoding such enzymes. The present invention meets thisneed, and further presents other related advantages.

SUMMARY OF THE INVENTION

[0010] The present invention provides isolated nucleic acids encodinghuman UDP-N-acetylglucosamine: N-acetylgalactosamine β1,6N-acetylglucosaminyltransferase 3 (C2GnT3), including cDNA and genomicDNA. C2GnT3 has acceptor substrate specificities comparable to C2GnT1(14). The complete nucleotide sequence encoding C2GnT3 is set forth inSEQ ID NO: 1 and in FIG. 1.

[0011] Variations in one or more nucleotides may exist among individualswithin a population due to natural allelic variation. Any and all suchnucleic acid variations are within the scope of the invention. DNAsequence polymorphisms may also occur which lead to changes in the aminoacid sequence of a C2GnT3 polypeptide. These amino acid polymorphismsare also within the scope of the present invention. In addition, speciesvariations i.e. variations in nucleotide sequence naturally occurringamong different species, are within the scope of the invention.

[0012] Among Core 2 β6GlcNAc-transferases, C2GnT3 appears to be thedominant isoform in thymus (14). Thus, C2GnT3 is likely to haveimportant functions during thymocyte development as well as T-cellmaturation and homing (14). The identification of agents with theability to inhibit or stimulate C2GnT3 enzymatic activity therefore hasthe potential for both diagnostic and therapeutic purposes of relateddiseases.

[0013] Access to the gene encoding C2GnT3 allows production of aglycosyltransferase for use in formation of core 2-based O-glycanmodifications on oligosacccharides, glycoproteins andglycosphingolipids. This enzyme can be used, for example, inpharmaceutical or other commercial applications that require syntheticaddition of core 2-based O-glycans to these or other substrates, inorder to produce appropriately glycosylated glycoconjugates havingparticular enzymatic, immunogenic, or other biological and/or physicalproperties.

[0014] In one aspect, the invention encompasses isolated nucleic acidscomprising the nucleotide sequence of nucleotides 1-1362 as set forth inFIG. 1 or sequence-conservative or function-conservative variantsthereof. Also provided are isolated nucleic acids hybridizable withnucleic acids having the sequence as set forth in FIG. 1 or fragmentsthereof or sequence-conservative or function-conservative variantsthereof; preferably, the nucleic acids are hybridizable with C2GnT3sequences under conditions of intermediate stringency, and, mostpreferably, under conditions of high stringency. In one embodiment, theDNA sequence encodes the amino acid sequence shown in FIG. 1, frommethionine (amino acid no. 1) to serine (amino acid no. 453). In anotherembodiment, the DNA sequence encodes an amino acid sequence comprising asequence from proline (no. 39) to serine (no.453) of the amino acidsequence set forth in FIG. 1.

[0015] In a related aspect, the invention provides nucleic acid vectorscomprising C2GnT3 DNA sequences, including but not limited to thosevectors in which the C2GnT3 DNA sequence is operably linked to atranscriptional regulatory element, with or without a polyadenylationsequence. Cells comprising these vectors are also provided, includingwithout limitation transiently and stably expressing cells. Viruses,including bacteriophages, comprising C2GnT3-derived DNA sequences arealso provided. The invention also encompasses methods for producingC2GnT3 polypeptides. Cell-based methods include without limitation thosecomprising: introducing into a host cell an isolated DNA moleculeencoding C2GnT3, or a DNA construct comprising a DNA sequence encodingC2GnT3; growing the host cell under conditions suitable for C2GnT3expression; and isolating C2GnT3 produced by the host cell. A method forgenerating a host cell with de novo stable expression of C2GnT3comprises: introducing into a host cell an isolated DNA moleculeencoding C2GnT3 or an enzymatically active fragment thereof (such as,for example, a polypeptide comprising amino acids 39-453 of the sequenceset forth FIG. 1), or a DNA construct comprising a DNA sequence encodingC2GnT3 or an enzymatically active fragment thereof; selecting andgrowing host cells in an appropriate medium; and identifying stablytransfected cells expressing C2GnT3. The stably transfected cells may beused for the production of C2GnT3 enzyme for use as a catalyst and forrecombinant production of peptides or proteins with appropriateglycosylation. For example, eukaryotic cells, whether normal or diseasedcells, having their glycosylation pattern modified by stabletransfection as above, or components of such cells, may be used todeliver specific glycoforms of glycopeptides and glycoproteins, such as,for example, as immunogens for vaccination.

[0016] In yet another aspect, the invention provides isolated C2GnT3polypeptides, including without limitation polypeptides having thesequence set forth in FIG. 1, polypeptides having the sequence of aminoacids 39-453 as set forth in FIG. 1, and a fusion polypeptide consistingof at least amino acids 39-453 as set forth in FIG. 1 fused in frame toa second sequence, which may be any sequence that is compatible withretention of C2GnT3 enzymatic activity in the fusion polypeptide.Suitable second sequences include without limitation those comprising anaffinity ligand or a reactive group.

[0017] In a related aspect, methods are disclosed for the identificationof agents with the ability to inhibit or stimulate the enzymaticactivity of C2GnT3. Assays utilizing C2GnT3 to screen for potentialinhibitors or stimulators thereof are encompassed by the invention.Furthermore, methods of using C2GnT3 in the structure-based design ofinhibitors or stimulators thereof are also an aspect of the invention.Such a design would comprise the steps of determining thethree-dimensional structure of the C2GnT3 polypeptide, analyzing thethree-dimensional structure for the likely binding sites of donor and /or acceptor substrates, synthesis of a molecule that incorporates apredictive reactive site, and determining the inhibiting or stimulatingactivity of the molecule.

[0018] In another aspect of the present invention, methods are disclosedfor screening for mutations in the coding region of the C2GnT3 geneusing genomic DNA isolated from, e.g., blood cells of patients. In oneembodiment, the method comprises: isolation of DNA from a patient; PCRamplification of the coding exon; DNA sequencing of amplified exon DNAfragments and establishing therefrom potential structural defects of theC2GnT3 gene associated with disease.

[0019] In accordance with an aspect of the invention there is provided amethod of, and products for (i.e. kits), diagnosing and monitoringconditions mediated by C2GnT3 by determining, in a biological sample,the presence of nucleic acid molecules and polypeptides of theinvention.

[0020] Still further the invention provides a method for evaluating atest compound for its ability to modulate the biological activity of aC2GnT3 polypeptide of the invention. For example, a substance thatinhibits or enhances the catalytic activity of a C2GnT3 polypeptide maybe evaluated. “Modulate” refers to a change or an alteration in thebiological activity of a polypeptide of the invention. Modulation may bean increase or a decrease in activity, a change in characteristics, orany other change in the biological, functional, or immunologicalproperties of the polypeptide.

[0021] Compounds which modulate the biological activity of a polypeptideof the invention may also be identified using the methods of theinvention by comparing the pattern and level of expression of a nucleicacid molecule or polypeptide of the invention in biological samples,tissues and cells, in the presence, and in the absence of the compounds.

[0022] In an embodiment of the invention a method is provided forscreening a compound for effectiveness as an antagonist of a polypeptideof the invention, comprising the steps of a) contacting a samplecontaining said polypeptide with a compound, under conditions whereinantagonist activity of said polypeptide can be detected, and b)detecting antagonist activity in the sample.

[0023] Methods are also contemplated that identify compounds orsubstances (e.g. polypeptides), which interact with C2GnT3 nucleic acidregulatory sequences (e.g. promoter sequences, enhancer sequences,negative modulator sequences).

[0024] The nucleic acids, polypeptides, and substances and compoundsidentified using the methods of the invention, may be used to modulatethe biological activity of a C2GnT3 polypeptide of the invention, andthey may be used in the treatment of conditions mediated by C2GnT3 suchas proliferative diseases including cancer, and thymus-relateddisorders. Accordingly, the nucleic acids, polypeptides, substances andcompounds may be formulated into compositions for administration toindividuals suffering from one or more of these conditions. Therefore,the present invention also relates to a composition comprising one ormore of a polypeptide, nucleic acid molecule, or substance or compoundidentified using the methods of the invention, and a pharmaceuticallyacceptable carrier, excipient or diluent. A method for treating orpreventing these conditions is also provided comprising administering toa patient in need thereof, a composition of the invention.

[0025] The present invention in another aspect provides means necessaryfor production of gene-based therapies directed at the thymus. Thesetherapeutic agents may take the form of polynucleotides comprising allor a portion of a nucleic acid of the invention comprising a regulatorysequence of a C2GnT3 nucleic acid placed in appropriate vectors ordelivered to target cells in more direct ways.

[0026] Having provided a novel C2GnT3, and nucleic acids encoding same,the invention accordingly further provides methods for preparingoligosaccharides. In specific embodiments, the invention relates to amethod for preparing an oligosaccharide comprising contacting a reactionmixture comprising a donor substrate, and an acceptor substrate in thepresence of a C2GnT3 polypeptide of the invention.

[0027] In accordance with a further aspect of the invention, there areprovided processes for utilizing polypeptides or nucleic acid molecules,for in vitro purposes related to scientific research, synthesis of DNA,and manufacture of vectors.

[0028] These and other aspects of the present invention will becomeevident upon reference to the following detailed description anddrawings.

BRIEF DESCRIPTION OF THE DRAWINGS

[0029]FIG. 1 depicts the DNA sequence of the C2GnT3 gene (accession #AF132035) and the predicted amino acid sequence of C2GnT3. The aminoacid sequence is shown in single letter code. The hydrophobic segmentrepresenting the putative transmembrane domain is double underlined.Four consensus motifs for N-glycosylation are indicated by asterisks.The location of the primers used for preparation of the expressionconstructs are indicated by single underlining.

[0030]FIG. 2 is an illustration of a sequence comparison between humanC2GnT3 (accession # AF132035; SEQ ID NO: 2), human C2GnT2 (formerlydesignated C2/4GnT; accession # AF038650; SEQ ID NO: 15), human C2GnT1(formerly designated C2GnT-L; accession # M97347; SEQ ID NO: 13), andhuman IGnT (accession # Z19550; SEQ ID NO: 17). Introduced gaps areshown as hyphens, and aligned identical residues are boxshaded (blackfor all sequences, dark grey for three sequences, and light grey for twosequences). The putative transmembrane domains are boxed. The positionsof conserved cysteines are indicated by asterisks. One conservedN-glycosylation site is indicated by an open circle. The correspondingnucleotide sequences are SEQ ID NO: 1 (C2GnT3), SEQ ID NO: 14 (C2GnT2),SEQ ID NO: 12 (C2GnT1), and SEQ ID NO: 16 (IGnT).

[0031]FIG. 3 depicts Northern blot analyses of healthy human adult andfetal tissues. Panel A: loading pattern for the human mRNA master blot(CLONTECH). Dots in row H contain 100 ng (H1-H7) or 500 ng (H8) ofcontrol DNA or RNA. Panel B: autoradiogram of master blot expressionanalysis using a ³²P-labeled C2GnT3 probe corresponding to the solubleexpression fragment of C2GnT3 (base pairs 115-1359). Panel C: A multiplehuman tissue northern blot (MTN II from Clontech) was probed asdescribed for panel B.

[0032]FIG. 4 shows a PCR analysis of C2GnT3 expression in human bloodcell fractions. PCR amplifications with primers specific for humanC2GnT3 (C2GnT3) or GAPDH (G3PDH) were performed on a normalized humanblood cell cDNA panel (MTC from Clontech) for 31 cycles.

[0033]FIG. 5 is a schematic representation of forward and reverse PCRprimers that can be used to amplify the coding exon of the C2GnT3 gene.The sequences of the primers TSHC119 and TSHC123 are also shown.

DETAILED DESCRIPTION OF THE INVENTION

[0034] All patent applications, patents, and literature references citedin this specification are hereby incorporated by reference in theirentirety. In the case of conflict, the present description, includingdefinitions, is intended to control.

DEFINITIONS

[0035] 1. “Nucleic acid” or “polynucleotide” as used herein refers topurine- and pyrimidine-containing polymers of any length, eitherpolyribonucleotides or polydeoxyribonucleotides or mixedpolyribo-polydeoxyribo nucleotides. This includes single- anddouble-stranded molecules, i.e., DNA-DNA, DNA-RNA and RNA-RNA hybrids,as well as “protein nucleic acids” (PNA) formed by conjugating bases toan amino acid backbone. This also includes nucleic acids containingmodified bases (see below).

[0036] 2. “Complementary DNA or cDNA” as used herein refers to a DNAmolecule or sequence that has been enzymatically synthesized from thesequences present in a mRNA template, or a clone of such a DNA molecule.A “DNA Construct” is a DNA molecule or a clone of such a molecule,either single- or double-stranded, which has been modified to containsegments of DNA that are combined and juxtaposed in a manner that wouldnot otherwise exist in nature. By way of non-limiting example, a cDNA orDNA which has no introns, ie., is free from non-coding sequences, isinserted adjacent to, or within, exogenous (e.g., heterologous) DNAsequences.

[0037] 3. A plasmid or, more generally, a vector or “expression vector”,is a DNA construct containing genetic information that may provide forits replication when inserted into a host cell. A plasmid generallycontains at least one gene sequence to be expressed in the host cell, aswell as sequences that facilitate such gene expression, includingpromoters and transcription initiation sites. It may be a linear orclosed circular molecule. Inserted coding sequences do not occurnaturally in the organism from which the vector is derived.

[0038] 4. Nucleic acids are “hybridizable” to each other when at leastone strand of one nucleic acid can anneal to another nucleic acid underdefined stringency conditions. Stringency of hybridization isdetermined, e.g., by a) the temperature at which hybridization and/orwashing is performed, and b) the ionic strength and polarity (e.g.,formamide) of the hybridization and washing solutions, as well as otherparameters. Hybridization requires that the two nucleic acids containsubstantially complementary sequences; depending on the stringency ofhybridization, however, mismatches may be tolerated. Typically,hybridization of two sequences at high stringency (such as, for example,in an aqueous solution of 0.5×SSC, at 65° C.) requires that thesequences exhibit some high degree of complementarity over their entiresequence. Conditions of intermediate stringency (such as, for example,an aqueous solution of 2×SSC at 65° C.) and low stringency (such as, forexample, an aqueous solution of 2×SSC at 55° C.), requirecorrespondingly less overall complementarily between the hybridizingsequences. (1×SSC is 0.15 M NaCl, 0.015 M Na citrate).

[0039] 5. An “isolated” nucleic acid or polypeptide as used hereinrefers to a component that is removed from its original environment (forexample, its natural environment if it is naturally occurring). Anisolated nucleic acid or polypeptide contains less than about 50%,preferably less than about 75%, and most preferably less than about 90%,of the cellular components with which it was originally associated.

[0040] 6. A “probe” refers to a nucleic acid that forms a hybridstructure with a sequence in a target region due to complementarily ofat least one sequence in the probe with a sequence in the target region.

[0041] 7. A nucleic acid that is “derived from” a designated sequencerefers to a nucleic acid sequence that corresponds to a region of thedesignated sequence. This encompasses sequences that are homologous orcomplementary to the sequence, as well as “sequence-conservativevariants” and “function-conservative variants”. Sequence-conservativevariants are those in which a change of one or more nucleotides in agiven codon position results in no alteration in the amino acid encodedat that position. Function-conservative variants of C2GnT3 are those inwhich a given amino acid residue in the polypeptide has been changedwithout altering the overall conformation and enzymatic activity(including substrate specificity) of the native polypeptide; thesechanges include, but are not limited to, replacement of an amino acidwith one having similar physico-chemical properties (such as, forexample, acidic, basic, hydrophobic, and the like).

[0042] 8. A “donor substrate” is a molecule recognized by, e.g., aCore-β1,6-N-acetylglucosaminyltransferase and that contributes anN-acetylglucosaminyl moiety for the transferase reaction. For C2GnT3, adonor substrate is UDP-N-acetylglucosamine. An “acceptor substrate” is amolecule, preferably a saccharide or oligosaccharide, that is recognizedby, e.g., an N-acetylglucosaminyltransferase and that is the target forthe modification catalyzed by the transferase, i.e., receives theN-acetylglucosaminyl moiety. For C2GnT3, acceptor substrates includewithout limitation oligosaccharides, glycoproteins, O-linked core1-glycopeptides, and glycosphingolipids comprising the sequencesGalβ1-3GalNAc, or GlcNAcβ1-3GalNAc.

[0043] 9. In accordance with the present invention there may be employedconventional molecular biology, microbiology, and recombinant DNAtechniques within the skill of the art. Such techniques are explainedfully in the literature. See for example, Sambrook, Fritsch, Maniatis,Molecular Cloning: A Laboratory Manual, Second Edition (1989) ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y.); DNA Cloning:A Practical Approach, Volumes I and II (D. N. Glover ed. 1985);Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic AcidHybridization B. D. Hames & S. J. Higgins eds. (1985); Transcription andTranslation B. D. Hames & S. J. Higgins eds (1984); Animal Cell CultureR. I. Freshney, ed. (1986); Immobilized Cells and enzymes IRL Press,(1986); and B. Perbal, A Practical Guide to Molecular Cloning (1984).

[0044] 10. The terms “sequence similarity” or “sequence identity” referto the relationship between two or more amino acid or nucleic acidsequences, determined by comparing the sequences, which relationship isgenerally known as “homology”. Identity in the art also means the degreeof sequence relatedness between amino acid or nucleic acid sequences, asthe case may be, as determined by the match between strings of suchsequences. Both identity and similarity can be readily calculated(Computational Molecular Biology, Lesk, A. M., ed., Oxford UniversityPress New York, 1988; Biocomputing: Informatics and Genome Projects,Smith, D. W. ed., Academic Press, New York, 1993; Computer Analysis ofSequence Data, Part I, Griffin, A. M., and Griffin, H. G. eds. HumanaPress, New Jersey, 1994; Sequence Analysis in Molecular Biology, vonHeinje, G., Academic Press, New York, 1987; and Sequence AnalysisPrimer, Gribskov, M. and Devereux, S., eds. M. Stockton Press, New York,1991). While there are a number of existing methods to measure identityand similarity between two amino acid sequences or two nucleic acidsequences, both terms are well known to the skilled artisan (SequenceAnalysis in Molecular Biology, von Hinge, G., Academic Press, New York,1987; Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds. M.Stockton Press, New York, 1991; and Carillo, H., and Lipman, D. SIAM J.Applied Math., 48.1073, 1988). Preferred methods for determiningidentity are designed to give the largest match between the sequencestested. Methods to determine identity are codified in computer programs.Preferred computer program methods for determining identity andsimilarity between two sequences include but are not limited to the GCGprogram package (20), BLASTP, BLASTN, and FASTA (21). Identity orsimilarity may also be determined using the alignment algorithm ofDayhoff et al. (Methods in Enzymology 91: 524-545 (1983)].

[0045] Preferably the nucleic acids of the present invention havesubstantial sequence identity using the preferred computer programscited herein, for example greater than 40%, 45%, 50%, 60%, 70%, 75%,80%, 85%, or 90% identity; more preferably at least 95%, 96%, 97%, 98%,or 99% sequence identity to the sequence shown in SEQ ID NO: 1 and FIG.1.

[0046] 11. The polypeptides of the invention also include homologs of aC2GnT3 polypeptide and/or truncations thereof as described herein. Suchhomologs include polypeptides whose amino acid sequences are comprisedof the amino acid sequences of C2GnT3 polypeptide regions from otherspecies that hybridize under selected hybridization conditions (seediscussion of hybridization conditions in particular stringenthybridization conditions herein) with a probe used to obtain a C2GnT3polypeptide or to SEQ ID NO:1. These homologs will generally have thesame regions which are characteristic of a C2GnT3 polypeptide. It isanticipated that a polypeptide comprising an amino acid sequence whichhas at least 40% identity, at least 45%, or at least 60% similarity,preferably at least 60-65% identity or at least 80-85% similarity, morepreferably at least 70-80% identity or at least 90-95% similarity, mostpreferably at least 95% identity or at least 99% similarity with theamino acid sequence shown in SEQ ID NO: 2 and FIGS. 1 and 2, will be ahomolog of a C2GnT3 polypeptide. A percent amino acid sequencesimilarity or identity is calculated using the methods described herein,preferably the computer programs described herein.

IDENTIFICATION AND CLONING OF C2GnT3

[0047] The present invention provides the isolated DNA molecules,including genomic DNA and cDNA, encoding the UDP-N-acetylglucosamine:N-acetylgalactosamine β1,6 N-acetylglucosaminyltransferase 3 (C2GnT3).

[0048] C2GnT3 was identified by analysis of genomic survey sequences(GSS), and cloned based on a genomic clone obtained from a humanforeskin fibroblast library. The cloning strategy may be brieflysummarized as follows: 1) isolation and sequencing of GSS cloneCIT-HSP-2288B17.TF (GSS GenBank accession number AQ005888); 2) synthesisof oligonucleotides derived from GSS sequence information, designatedTSHC96 and TSHC101; 3) identification, cloning and sequencing of genomicP1 clone GS22597 #844/B1; 4) identification of a novel cDNA sequencecorresponding to C2GnT3; 5) confirmatory sequencing of a cDNA cloneobtained by reverse-transcription-polymerase chain reaction (RT-PCR)using human thymus poly A-mRNA; 6) construction of expressionconstructs; 7) expression of the cDNA encoding C2GnT3 in Sf9 (Spodopterafrugiperda) cells. More specifically, the isolation of a representativeDNA molecule encoding a novel third member of the mammalianUDP-N-acetylglucosamine: β-N-actylgalactosamineβ1,6-N-acetylglucosaminyltransferase family involved the followingprocedures described below.

Identification of DNA Homologous to C2/4GnT (C2GnT2)

[0049] Database searches were performed with the coding sequence of thehuman C2/4GnT (C2GnT2) sequence (13) using the BLASTn and the tBLASTnalgorithm with the GSS database at The National Center for BiotechnologyInformation, USA. The BLASTn algorithm was used to identify clonesrepresenting the query gene (identities of ≧95%), whereas tBLASTn wasused to identify non-identical, but similar GSS sequences. GSSs with50-90% nucleotide sequence identity were regarded as different from thequery sequence. Two GSS clones with several apparent short sequencemotifs and cysteine residues arranged with similar spacing were selectedfor further sequence analysis.

Cloning of Human C2GnT3

[0050] GSS clone CIT-HSP-2288B17.TF (GSS GenBank accession numberAQ005888), derived from a putative homologue to C2/4GnT (C2GnT2), wasobtained from Research Genetics Inc., USA. Sequencing of this clonerevealed a partial open reading frame with significant sequencesimilarity to C2/4GnT (C2GnT2). The coding region of human C2GnT-L(C2GnT1), C2/4GnT (C2GnT2) and a bovine homologue was previously foundto be organized in one exon ((22),(15)). Since the 3′ sequence availablefrom the C2GnT3 GSS was incomplete but likely to be located in a singleexon, the missing 3′ portion of the open reading frame was obtained bysequencing a genomic P1 clone. The P1 clone was obtained from a humanforeskin genomic P1 library (DuPont Merck Pharmaceutical Co. HumanForeskin Fibroblast P1 Library) by screening with the primer pair:TSHC96 (5′-GGTTTCACCGTCTCCAACATA-3′, SEQ ID NO:3) and TSHC101(5′-TCGTAAGGCACCTGATACTT-3′, SEQ ID NO:6).

[0051] One genomic clone for C2GnT3, GS22597 #844/B1 was obtained fromGenome Systems Inc. DNA from P1 phage was prepared as recommended byGenome Systems Inc. The entire coding sequence of the C2GnT3 gene wasrepresented in the clone and sequenced in full using automatedsequencing (ABI377, Perkin-Elmer). Confirmatory sequencing was performedon a cDNA clone obtained by PCR (30 cycles at 95° C. for 10 sec; 55° C.for 15 sec and 68° C. for 2 min 30 sec) on cDNA from human thymus polyA-mRNA with the sense primer: TSHC99(5′-CGAGGATCCAGAATGAAGATATTCAAATGTTA-3′, SEQ ID NO:4), and theanti-sense primer TSHC121 (5′-AGCGAATTCTTACTATCATGATGTGGTAGTG-3′, SEQ IDNO:9).

[0052] The composite sequence contained an open reading frame of 1359base pairs encoding a putative protein of 453 amino acids with type IIdomain structure predicted by the TMpred-algorithm at the SwissInstitute for Experimental Cancer Research (ISREC).

[0053] (http://www.ch.embnet.org/software/TMPRED_form.html).

Expression of C2GnT3

[0054] An expression construct designed to encode amino acid residues39-453 of C2GnT3 was prepared by PCR using P1 DNA, and the primer pair:TSHC100 (5′-CGAGGATCCGCAAAAAGACATTTACTTGGTT-3′, SEQ ID NO:5) and TSHC121(5′-AGCGAATTCTTACTATCATGATGTGGTAGTG-3′, SEQ ID NO:9)

[0055] with BamH1 and EcoRI restriction sites, respectively (FIG. 2).The PCR product was cloned between the BamHI and EcoRI sites of pAcGP67A(PharMingen), and the insert was fully sequenced. pAcGP67-C2GnT3-sol wasco-transfected with Baculo-Gold™ DNA (PharMingen) as describedpreviously (23). Recombinant Baculovirus was obtained after twosuccessive amplifications in Sf9 cells grown in serum-containing medium,and titers of virus were estimated by titration in 24-well plates withmonitoring of enzyme activities. Transfection of Sf9-cells withpAcGP67-C2GnT3-sol resulted in marked increase in GlcNAc-transferaseactivity compared to uninfected cells or cells infected with a controlconstruct. C2GnT3 showed significant activity with disaccharidederivatives of O-linked core 1 (Galβ1-3GalNAcα1-R). In contrast, noactivity was found with core 3 structures (GlcNAcβ1-3GalNAcα1-R),lacto-N-neotetraose as well as GlcNAcβ1-3Gal-Me as acceptor substratesindicating that C2GnT3 has no Core4GnT and IGnT-activity. Additionally,no activity could be detected wih α-D-GalNAc-1- para-nitrophenylindicating that C2GnT3 does not form core 6 (GlcNAcβ1-6GalNAcα1-R)(Table I). No substrate inhibition of enzyme activity was found at highacceptor concentrations up to 20 mM core 1-par-nitrophenyl. C2GnT3 showsstrict donor substrate specificity for UDP-GlcNAc, no activity could bedetected with UDP-Gal or UDP-GaiNAc (data not shown). TABLE I Substratespecificities of C2GnT3 and C2GnT1 C2GnT3^(a) C2GnT1 Substrate 2 mM 10mM 2 mM 10 mM nmol/h/mg nmol/h/mg β-D-Gal-(1-3)-α-D-GalNAc 6.6 14.3 9.619.0 β-D-Gal-(1-3)-α-D-GalNAc-1-p-Nph 18.1 26.1 16.2 23.6β-D-GlcNAc-(1-3)-α-D-GalNAc-1-p-Nph <0.1 <0.1 <0.1 <0.1α-D-GalNAc-1-p-Nph <0.1 <0.1 <0.1 <0.1 D-GalNAc <0.1 <0.1 <0.1 <0.1lacto-N-neo-tetraose <0.1 <0.1 <0.1 <0.1 β-D-GlcNAc-(1-3)-β-D-Gal-1-Me<0.1 <0.1 <0.1 <0.1

[0056] Controls included the pAcGP67-GalNAc-T3-sol (24). The kineticproperties were determined with partially purified enzymes expressed inHigh Five™ cells. Partial purification was performed by consecutivechromatography on Amberlite IRA-95, DEAE-Sephacryl and SP-Sepharoseessentially as described (25; 25).

Northern Blot Analysis of Human Organs

[0057] A human RNA master blot containing mRNA from fifty healthy humanadult and fetal organs (CLONTECH) and a human multiple tissue northernblot (MTNII from CLONTECH) were probed with a ³²P-labeled probecorresponding to the soluble fragment of C2GnT3 (base pairs 115-1359).The autoradiographic analyses showed expression of C2GnT3 predominantlyin lymphoid organs and in organs of the gastrointestinal tract with hightranscription levels observed in thymus, and lower levels in PBLs, lymphnode, stomach, pancreas and small intestine (FIG. 3A and 3B). The sizeof the single transcript was approximately 5.5 kilobases, whichcorrelates to the transcript size of 5.4 kilobases of the biggest ofthree transcripts of human C2GnT1 (FIG. 3C). Multiple transcripts ofC2GnT1 have been suggested to be caused by differential usage ofpolyadenylation signals, which affects the length of the 3′ UTR (13).

[0058] The C2GnT3 enzyme of the present invention was shown to exhibitO-glycosylation capacity implying that the C2GnT3 gene is vital forcorrect/full O-glycosylation in vivo as well. A structural defect in theC2GnT3 gene leading to a deficient enzyme or completely defective enzymewould therefore expose a cell or an organism to protein/peptidesequences which were not covered by O-glycosylation as seen in cells ororganisms with intact C2GnT3 gene. Described in Example 5 below is amethod for scanning the coding exon for potential structural defects.Similar methods could be used for the characterization of defects in thenon-coding region of the C2GnT3 gene including the promoter region.

DNA, Vectors, and Host Cells

[0059] In practicing the present invention, many conventional techniquesin molecular biology, microbiology, recombinant DNA, and immunology, areused. Such techniques are well known and are explained fully in, forexample, Sambrook et al., 1989, Molecular Cloning A Laboratory Manual,Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y.; DNA Cloning: A Practical Approach, Volumes I and II, 1985 (D. N.Glover ed.); Oligonucleotide Synthesis, 1984, (M. L. Gait ed.); NucleicAcid Hybridization, 1985, (Hames and Higgins); Transcription andTranslation, 1984 (Hames and Higgins eds.); Animal Cell Culture, 1986(R. I. Freshney ed.); Immobilized Cells and Enzymes, 1986 (IRL Press);Perbal, 1984, A Practical Guide to Molecular Cloning; the series,Methods in Enzymology (Academic Press, Inc.); Gene Transfer Vectors forMammalian Cells, 1987 (J. H. Miller and M. P. Calos eds., Cold SpringHarbor Laboratory); Methods in Enzymology Vol. 154 and Vol. 155 (Wu andGrossman, and Wu, eds., respectively); Immunochemical Methods in Celland Molecular Biology, 1987 (Mayer and Waler, eds; Academic Press,London); Scopes, 1987, Protein Purification: Principles and Practice,Second Edition (Springer-Verlag, N.Y.) and Handbook of ExperimentalImmunology, 1986, Volumes I-IV (Weir and Blackwell eds.).

[0060] The invention encompasses isolated nucleic acid fragmentscomprising all or part of the nucleic acid sequence disclosed herein asset forth in FIG. 1. The fragments are at least about 8 nucleotides inlength, preferably at least about 12 nucleotides in length, and mostpreferably at least about 15-20 nucleotides in length. The inventionfurther encompasses isolated nucleic acids comprising sequences that arehybridizable under stringency conditions of 2×SSC, 55° C., to thesequence set forth in FIG. 1; preferably, the nucleic acids arehybridizable at 2×SSC, 65° C.; and most preferably, are hybridizable at0.5×SSC, 65° C.

[0061] The nucleic acids may be isolated directly from cells.Alternatively, the polymerase chain reaction (PCR) method can be used toproduce the nucleic acids of the invention, using either chemicallysynthesized strands or genomic material as templates. Primers used forPCR can be synthesized using the sequence information provided hereinand can further be designed to introduce appropriate new restrictionsites, if desirable, to facilitate incorporation into a given vector forrecombinant expression.

[0062] The nucleic acids of the present invention may be flanked bynatural human regulatory sequences, or may be associated withheterologous sequences, including transcriptional control elements suchas promoters, enhancers, and response elements, or other sequences suchas signal sequences, polyadenylation sequences, introns, 5′- and 3′-noncoding regions, and the like. Preferably, although not necessarily,any two nucleotide sequences to be expressed as a fusion polypeptide areinserted in-frame. The nucleic acids may also be modified by many meansknown in the art. Non-limiting examples of such modifications includemethylation, “caps”, substitution of one or more of the naturallyoccurring nucleotides with an analog, internucleotide modifications suchas, for example, those with uncharged linkages (e.g., methylphosphonates, phosphotriesters, phosphoroamidates, carbamates, etc.) andwith charged linkages (e.g., phosphorothioates, phosphorodithioates,etc.).

[0063] Nucleic acids may contain one or more additional covalentlylinked moieties, such as, for example, proteins (e.g., nucleases,toxins, antibodies, signal peptides, poly-L-lysine, etc.), intercalators(e.g., acridine, psoralen, etc.), chelators (e.g., metals, radioactivemetals, iron, oxidative metals, etc.), and alkylators. The nucleic acidmay be derivatized by formation of a methyl or ethyl phosphotriester oran alkyl phosphoramidate linkage. Furthermore, the nucleic acidsequences of the present invention may also be modified with a labelcapable of providing a detectable signal, either directly or indirectly.Exemplary labels include radioisotopes, fluorescent molecules, biotin,and the like.

[0064] According to the present invention, useful probes comprise aprobe sequence at least eight nucleotides in length that consists of allor part of the sequence from among the sequences as set forth in FIG. 1or sequence-conservative or function-conservative variants thereof, or acomplement thereof, and that has been labelled as described above.

[0065] The invention also provides nucleic acid vectors comprising thedisclosed sequence or derivatives or fragments thereof. A large numberof vectors, including plasmid and fungal vectors, have been describedfor replication and/or expression in a variety of eukaryotic andprokaryotic hosts, and may be used for gene therapy as well as forsimple cloning or protein expression.

[0066] Recombinant cloning vectors will often include one or morereplication systems for cloning or expression, one or more markers forselection in the host, e.g. antibiotic resistance, and one or moreexpression cassettes. The inserted coding sequences may be synthesizedby standard methods, isolated from natural sources, or prepared ashybrids, etc. Ligation of the coding sequences to transcriptionalregulatory elements and/or to other amino acid coding sequences may beachieved by known methods. Suitable host cells may betransformed/transfected/infected as appropriate by any suitable methodincluding electroporation, CaCl₂ mediated DNA uptake, fungal infection,microinjection, microprojectile, or other established methods.

[0067] Appropriate host cells included bacteria, archaebacteria, fungi,especially yeast, and plant and animal cells, especially mammaliancells. Also included are avian and insect cells. Of particular interestare Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichiapastoris, Hansenula polymorpha, Neurospora spec., SF9 cells, C129 cells,293 cells, and CHO cells, COS cells, HeLa cells, and immortalizedmammalian myeloid and lymphoid cell lines. Preferred replication systemsinclude M13, ColE1, 2μ, ARS, SV40, baculovirus, lambda, adenovirus, andthe like. A large number of transcription initiation and terminationregulatory regions have been isolated and shown to be effective in thetranscription and translation of heterologous proteins in the varioushosts.

[0068] Examples of these regions, methods of isolation, manner ofmanipulation, etc. are known in the art. Under appropriate expressionconditions, host cells can be used as a source of recombinantly producedC2GnT3 derived peptides and polypeptides.

[0069] Advantageously, vectors may also include a transcriptionregulatory element (i.e., a promoter) operably linked to the C2GnT3coding portion. The promoter may optionally contain operator portionsand/or ribosome binding sites. Non-limiting examples of bacterialpromoters compatible with E. coli include: β-lactamase (penicillinase)promoter; lactose promoter; tryptophan (trp) promoter; arabinose BADoperon promoter; lambda-derived P₁ promoter and N gene ribosome bindingsite; and the hybrid tac promoter derived from sequences of the trp andlac UV5 promoters. Non-limiting examples of yeast promoters include3-phosphoglycerate kinase promoter, glyceraldehyde-3 phosphatedehydrogenase (GAPDH) promoter, galactokinase (GAL1) promoter,galactoepimerase (GAL10) promoter, metallothioneine (CUP) promoter andalcohol dehydrogenase (ADH) promoter. Suitable promoters for mammaliancells include without limitation viral promoters such as that fromSimian Virus 40 (SV40), Rous sarcoma virus (RSV), adenovirus (ADV), andbovine papilloma virus (BPV). Mammalian cells may also requireterminator sequences and poly A addition sequences and enhancersequences which increase expression may also be included; sequenceswhich cause amplification of the gene may also be desirable.Furthermore, sequences that facilitate secretion of the recombinantproduct from cells, including, but not limited to, bacteria, yeast, andanimal cells, such as secretory signal sequences and/or prohormone proregion sequences, may also be included. These sequences are known in theart.

[0070] Nucleic acids encoding wild type or variant polypeptides may alsobe introduced into cells by recombination events. For example, such asequence can be introduced into a cell, and thereby effect homologousrecombination at the site of an endogenous gene or a sequence withsubstantial identity to the gene. Other recombination-based methods suchas nonhomologous recombinations or deletion of endogenous genes byhomologous recombination may also be used.

[0071] The nucleic acids of the present invention find use, for example,as probes for the detection of C2GnT3 in other species or relatedorganisms and as templates for the recombinant production of peptides orpolypeptides. These and other embodiments of the present invention aredescribed in more detail below.

Polypeptides and Antibodies

[0072] The present invention encompasses isolated peptides andpolypeptides encoded by the disclosed cDNA sequence. Peptides arepreferably at least five residues in length.

[0073] Nucleic acids comprising protein-coding sequences can be used todirect the recombinant expression of polypeptides in intact cells or incell-free translation systems. The known genetic code, tailored ifdesired for more efficient expression in a given host organism, can beused to synthesize oligonucleotides encoding the desired amino acidsequences. The phosphoramidite solid support method of (26), the methodof (27), or other well known methods can be used for such synthesis. Theresulting oligonucleotides can be inserted into an appropriate vectorand expressed in a compatible host organism.

[0074] The polypeptides of the present invention, includingfunction-conservative variants of the disclosed sequence, may beisolated from native or from heterologous organisms or cells (including,but not limited to, bacteria, fungi, insect, plant, and mammalian cells)into which a protein-coding sequence has been introduced and expressed.Furthermore, the polypeptides may be part of recombinant fusionproteins.

[0075] Methods for polypeptide purification are well known in the art,including, without limitation, preparative discontiuous gelelctrophoresis, isoelectric focusing, HPLC, reversed-phase HPLC, gelfiltration, ion exchange and partition chromatography, andcountercurrent distribution. For some purposes, it is preferable toproduce the polypeptide in a recombinant system in which the proteincontains an additional sequence tag that facilitates purification, suchas, but not limited to, an affinity ligand, reactive group, and/or apolyhistidine sequence. The polypeptide can then be purified from acrude lysate of the host cell by chromatography on an appropriatesolid-phase matrix. Alternatively, antibodies produced against a proteinor against peptides derived therefrom can be used as purificationreagents. Other purification methods are possible.

[0076] The present invention also encompasses derivatives and homologuesof polypeptides. For some purposes, nucleic acid sequences encoding thepeptides may be altered by substitutions, additions, or deletions thatprovide for functionally equivalent molecules, i.e.,function-conservative variants. For example, one or more amino acidresidues within the sequence can be substituted by another amino acid ofsimilar properties, such as, for example, positively charged amino acids(arginine, lysine, and histidine); negatively charged amino acids(aspartate and glutamate); polar neutral amino acids; and non-polaramino acids.

[0077] The isolated polypeptides may be modified by, for example,phosphorylation, sulfation, acylation, or other protein modifications.They may also be modified with a label capable of providing a detectablesignal, either directly or indirectly, including, but not limited to,radioisotopes and fluorescent compounds.

[0078] The present invention encompasses antibodies that specificallyrecognize immunogenic components derived from C2GnT3. Such antibodiescan be used as reagents for detection and purification of C2GnT3.

[0079] C2GnT3 specific antibodies according to the present inventioninclude polyclonal and monoclonal antibodies. The antibodies may beelicited in an animal host by immunization with C2GnT3 components or maybe formed by in vitro immunization of immune cells. The immunogeniccomponents used to elicit the antibodies may be isolated from humancells or produced in recombinant systems. The antibodies may also beproduced in recombinant systems programmed with appropriateantibody-encoding DNA. Alternatively, the antibodies may be constructedby biochemical reconstitution of purified heavy and light chains. Theantibodies include hybrid antibodies (i.e., containing two sets of heavychain/light chain combinations, each of which recognizes a differentantigen), chimeric antibodies (i.e., in which either the heavy chains,light chains, or both, are fusion proteins), and univalent antibodies(i.e., comprised of a heavy chain/light chain complex bound to theconstant region of a second heavy chain). Also included are Fabfragments, including Fab′ and F(ab)₂ fragments of antibodies. Methodsfor the production of all of the above types of antibodies andderivatives are well known in the art. For example, techniques forproducing and processing polyclonal antisera are disclosed in Mayer andWalker, 1987, Immunochemical Methods in Cell and Molecular Biology,(Academic Press, London).

[0080] The antibodies of this invention can be purified by standardmethods, including but not limited to preparative disc-gelelctrophoresis, isoelectric focusing, HPLC, reversed-phase HPLC, gelfiltration, ion exchange and partition chromatography, andcountercurrent distribution. Purification methods for antibodies aredisclosed, e.g., in The Art of Antibody Purification, 1989, AmiconDivision, W. R. Grace & Co. General protein purification methods aredescribed in Protein Purification: Principles and Practice, R. K.Scopes, Ed., 1987, Springer-Verlag, New York, N.Y.

[0081] Anti C2GnT3 antibodies, whether unlabeled or labeled by standardmethods, can be used as the basis for immunoassays. The particular labelused will depend upon the type of immunoassay used. Examples of labelsthat can be used include, but are not limited to, radiolabels such as³²P, ¹²⁵I, ³H and ¹⁴C; fluorescent labels such as fluorescein and itsderivatives, rhodamine and its derivatives, dansyl and umbelliferone;chemiluminescers such as luciferia and 2,3-dihydrophthalazinediones; andenzymes such as horseradish peroxidase, alkaline phosphatase, lysozymeand glucose-6-phosphate dehydrogenase.

[0082] The antibodies can be tagged with such labels by known methods.For example, coupling agents such as aldehydes, carbodiimides,dimaleimide, imidates, succinimides, bisdiazotized benzadine and thelike may be used to tag the antibodies with fluorescent,chemiluminescent or enzyme labels. The general methods involved are wellknown in the art and are described in, e.g., Chan (Ed.), 1987,Immunoassay: A Practical Guide, Academic Press, Inc., Orlando, Fla.

APPLICATIONS OF THE NUCLEIC ACID MOLECULES, POLYPEPTIDES, AND ANTIBODIESOF THE INVENTION

[0083] The nucleic acid molecules, C2GnT3 polypeptide, and antibodies ofthe invention may be used in the prognostic and diagnostic evaluation ofconditions associated with altered expression or activity of apolypeptide of the invention or conditions requiring modulation of anucleic acid or polypeptide of the invention including thymus-relateddisorders and proliferative disorders (e.g. cancer), and theidentification of subjects with a predisposition to such conditions (Seebelow). Methods for detecting nucleic acid molecules and polypeptides ofthe invention can be used to monitor such conditions by detecting andlocalizing the polypeptides and nucleic acids. It would also be apparentto one skilled in the art that the methods described herein may be usedto study the developmental expression of the polypeptides of theinvention and, accordingly, will provide further insight into the roleof the polypeptides. The applications of the present invention alsoinclude methods for the identification of substances or compounds thatmodulate the biological activity of a polypeptide of the invention (Seebelow). The substances, compounds, antibodies etc., may be used for thetreatment of conditions requiring modulation of polypeptides of theinvention (See below).

Diagnostic Methods

[0084] A variety of methods can be employed for the diagnostic andprognostic evaluation of conditions requiring modulation of a nucleicacid or polypeptide of the invention (e.g. thymus-related disorders, andcancer), and the identification of subjects with a predisposition tosuch conditions. Such methods may, for example, utilize nucleic acids ofthe invention, and fragments thereof, and antibodies directed againstpolypeptides of the invention, including peptide fragments. Inparticular, the nucleic acids and antibodies may be used, for example,for: (1) the detection of the presence of C2GnT3 mutations, or thedetection of either over- or under-expression of C2GnT3 mRNA relative toa non-disorder state or the qualitative or quantitative detection ofalternatively spliced forms of C2GnT3 transcripts which may correlatewith certain conditions or susceptibility toward such conditions; or (2)the detection of either an over- or an under-abundance of a polypeptideof the invention relative to a non-disorder state or the presence Of amodified (e.g., less than full length) polypeptide of the inventionwhich correlates with a disorder state, or a progression toward adisorder state.

[0085] The methods described herein may be performed by utilizingpre-packaged diagnostic kits comprising at least one specific nucleicacid or antibody described herein, which may be conveniently used, e.g.,in clinical settings, to screen and diagnose patients and to screen andidentify those individuals exhibiting a predisposition to developing adisorder.

[0086] Nucleic acid-based detection techniques and peptide detectiontechniques are described below. The samples that may be analyzed usingthe methods of the invention include those that are known or suspectedto express C2GnT3 nucleic acids or contain a polypeptide of theinvention. The methods may be performed on biological samples includingbut not limited to cells, lysates of cells which have been incubated incell culture, chromosomes isolated from a cell (e.g. a spread ofmetaphase chromosomes), genomic DNA (in solutions or bound to a solidsupport such as for Southern analysis), RNA (in solution or bound to asolid support such as for northern analysis), cDNA (in solution or boundto a solid support), an extract from cells or a tissue, and biologicalfluids such as serum, urine, blood, and CSF. The samples may be derivedfrom a patient or a culture.

Methods for Detection of Nucleic Acid Molecules of the Invention

[0087] The nucleic acid molecules of the invention allow those skilledin the art to construct nucleotide probes for use in the detection ofnucleic acid sequences of the invention in biological materials.Suitable probes include nucleic acid molecules based on nucleic acidsequences encoding at least 5 sequential amino acids from regions of theC2GnT3 polypeptide (see SEQ ID NO: 1), preferably they comprise 15 to 50nucleotides, more preferably 15 to 40 nucleotides, most preferably 15-30nucleotides. A nucleotide probe may be labelled with a detectablesubstance such as a radioactive label that provides for an adequatesignal and has sufficient half-life such as ³²P, ³H, ¹⁴C or the like.Other detectable substances that may be used include antigens that arerecognized by a specific labelled antibody, fluorescent compounds,enzymes, antibodies specific for a labelled antigen, and luminescentcompounds. An appropriate label may be selected having regard to therate of hybridization and binding of the probe to the nucleotide to bedetected and the amount of nucleotide available for hybridization.Labelled probes may be hybridized to nucleic acids on solid supportssuch as nitrocellulose filters or nylon membranes as generally describedin Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual (2nded.). The nucleic acid probes may be used to detect C2GnT3 genes,preferably in human cells. The nucleotide probes may also be used forexample in the diagnosis or prognosis of conditions such asthymus-related disorders and cancer, and in monitoring the progressionof these conditions, or monitoring a therapeutic treatment.

[0088] The probe may be used in hybridisation techniques to detect aC2GnT3 gene. The technique generally involves contacting and incubatingnucleic acids (e.g. recombinant DNA molecules, cloned genes) obtainedfrom a sample from a patient or other cellular source with a probe ofthe present invention under conditions favourable for the specificannealing of the probes to complementary sequences in the nucleic acids.Alter incubation, the non-annealed nucleic acids are removed, and thepresence of nucleic acids that have hybridized to the probe if any aredetected.

[0089] The detection of nucleic acid molecules of the invention mayinvolve the amplification of specific gene sequences using anamplification method (e.g. PCR), followed by the analysis of theamplified molecules using techniques known to those skilled in the art.Suitable primers can be routinely designed by one of skill in the art.For example, primers may be designed using commercially availablesoftware, such as OLIGO 4.06 Primer Analysis software (NationalBiosciences, Plymouth, Minn.) or another appropriate program, to beabout 22 to 30 nucleotides in length, to have a GC content of about 50%or more, and to anneal to the template at temperatures of about 60° C.to 72° C.

[0090] Genomic DNA may be used in hybridization or amplification assaysof biological samples to detect abnormalities involving C2GnT3 nucleicacid structure, including point mutations, insertions, deletions, andchromosomal rearrangements. For example, direct sequencing, singlestranded conformational polymorphism analyses, heteroduplex analysis,denaturing gradient gel electrophoresis, chemical mismatch cleavage, andoligonucleotide hybridization may be utilized.

[0091] Genotyping techniques known to one skilled in the art can be usedto type polymorphisms that are in close proximity to the mutations in aC2GnT3 gene. The polymorphisms may be used to identify individuals infamilies that are likely to carry mutations. If a polymorphism exhibitslinkage disequalibrium with mutations in the G2GnT3 gene, it can also beused to screen for individuals in the general population likely to carrymutations. Polymorphisms which may be used include restriction fragmentlength polymorphisms (RFLPs), single-nucleotide polymorphisms (SNP), andsimple sequence repeat polymorphisms (SSLPs).

[0092] A probe or primer of the invention may be used to directlyidentify RFLPs. A probe or primer of the invention can additionally beused to isolate genomic clones such as YACs, BACs, PACs, cosmids, phageor plasmids. The DNA in the clones can be screened for SSLPs usinghybridization or sequencing procedures.

[0093] Hybridization and amplification techniques described herein maybe used to assay qualitative and quantitative aspects of C2GnT3expression. For example RNA may be isolated from a cell type or tissueknown to express C2GnT3 and tested utilizing the hybridization (e.g.standard Northern analyses) or PCR techniques referred to herein. Thetechniques may be used to detect differences in transcript size that maybe doe to normal or abnormal alternative splicing. The techniques may beused to detect quantitative differences between levels of full lengthand/or alternatively splice transcripts detected in normal individualsrelative to those individuals exhibiting symptoms of a disease.

[0094] The primers and probes may be used in the above described methodsin situ i.e directly on tissue sections (fixed and/or frozen) of patienttissue obtained from biopsies or resections.

[0095] Oligonucleotides or longer fragments derived from any of thenucleic acid molecules of the invention may be used as targets in amicroarray. The microarray can be used to simultaneously monitor theexpression levels of large numbers of genes and to identify geneticvariants, mutations, and polymorphisms. The information from themicroarray may be used to determine gene function, to understand thegenetic basis of a disorder, to identify predisposition to a disorder,to treat a disorder, to diagnose a disorder, and to develop and monitorthe activities of therapeutic agents.

[0096] The preparation, use, and analysis of micro arrays are well knownto a person skilled in the art. (see, for example, Brennan, T. M., etal. (1995), U.S. Pat. No. 5,474,796; Schena et al. (1996), Proc. Natl.Acad. Sci. 93:10614-10619; Baldeschweiler et al. (1995), PCT ApplicationWO95/251116; Shalon, D., et al. (1995), PCT application WO95/35505;Heller, R. A., et al. (1997), Proc. Natl. Acad. Sci. 94:2150-2155; andHeller, M. J., et al. (1997), U.S. Pat. No. 5,605,662.)

Methods for Detecting Polypeptides

[0097] Antibodies specifically reactive with a C2GnT3 Polypeptide, orderivatives, such as enzyme conjugates or labeled derivatives, may beused to detect C2GnT3 polypeptides in various biological materials. Theymay be used as diagnostic or prognostic reagents and they may be used todetect abnormalities in the level of C2GnT3 polypeptides, expression, orabnormalities in the structure, and/or temporal, tissue, cellular, orsubcellular location of the polypeptides. Antibodies may also be used toscreen potentially therapeutic compounds in vitro to determine theireffects on a condition such as a thymus-related disorder or cancer. Invitro immunoassays may also be used to assess or monitor the efficacy ofparticular therapies. Preferably, antibodies for use in a detectionassay have a dissociation constant lower than 1 μM, even more preferablylower than or about 10 nM.

[0098] The antibodies of the invention may also be used in vitro todetermine the level of C2GnT3 polypeptide expression in cellsgenetically engineered to produce a C2GnT3 polypeptide. The antibodiesmay be used to detect and quantify polypeptides of the invention in asample in order to determine their role in particular cellular events orpathological states, and to diagnose and treat such pathological states.

[0099] In particular, the antibodies of the invention may be used inimmuno-histochemical analyses, for example, at the cellular andsub-subcellular level, to detect a polypeptide of the invention, tolocalize it to particular cells and tissues, and to specific subcellularlocations, and to quantitate the level of expression.

[0100] The antibodies may be used in any known immunoassays that rely onthe binding interaction

between an antigenic determinant of a polypeptide of the invention, andthe antibodies. Examples of such assays are radio immunoassays, enzymeimmunoassays (e.g. ELISA), immunofluorescence, immunoprecipitation,latex agglutination, hemagglutination, and histochemical tests,

[0101] Cytochemical techniques known in the art for localizing antigensusing light and electron microscopy may be used to detect a polypeptideof the invention. Generally, an antibody of the invention may belabelled with a detectable substance and a polypeptide may be localisedin tissues and cells based upon the presence of the detectablesubstance. Various methods of labelling polypeptides are known in theart and may be used. Examples of detectable substances include, but arenot limited to, the following: radioisotopes (e.g., ³H, ¹⁴C, ³⁵S, ¹²⁵I,¹³¹I), fluorescent labels (e.g., FITC, Rhodamine, lanthanide phosphors),luminescent labels such as luminol, enzymatic labels (e.g., horseradishperoxidase, β-galactosidase, luciferase, alkaline phosphatase,acetylcholinesterase), biotinyl groups (which can be detected by markedavidin e.g., streptavidin containing a fluorescent marker or enzymaticactivity that can be detected by optical or calorimetric methods),predetermined polypeptide epitopes recognized by a secondary reporter(e.g., leucine zipper pair sequences, binding sites for secondaryantibodies, metal binding domains, epitope tags). In some embodiments,labels are attached via spacer arms of various lengths to reducepotential steric hindrance. Antibodies may also be coupled to electrondense substances, such as ferritin or colloidal gold, which are readilyvisualised by electron microscopy.

[0102] The antibody or sample may be immobilized on a carrier or solidsupport which is capable of immobilizing cells, antibodies, etc. Forexample, the carrier or support may be nitrocellulose, or glass,polyacrylamides, gabbros, and magnetite. The support material may haveany possible configuration including spherical (e.g. bead), cylindrical(e.g. inside surface of a test tube or well, or the external surface ofa rod), or flat (e.g. sheet, test strip). Indirect methods may also beemployed in which the primary antigen-antibody reaction is amplified bythe introduction of a second antibody, having specificity for theantibody reactive against a polypeptide of the invention. By way ofexample, if the antibody having specificity against a polypeptide of theinvention is a rabbit IgG antibody, the second antibody may be goatanti-rabbit gamma-globulin labelled with a detectable substance asdescribed herein.

[0103] Where a radioactive label is used as a detectable substance, apolypeptide of the invention may be localized by radioautography. Theresults of radioautography may be quantitated by determining the densityof particles in the radioautographs by various optical methods, or bycounting the grains.

[0104] A polypeptide of the invention may also be detected by assayingfor C2GnT3 activity as described herein. For example, a sample may bereacted with an acceptor substrate and a donor substrate underconditions where a C2GnT3 polypeptide is capable of transferring thedonor substrate to the acceptor substrate to produce a donorsubstrate-acceptor substrate complex.

Methods for Identifying or Evaluating Substances/Compounds

[0105] The methods described herein are designed to identify substancesand compounds that modulate the expression or biological activity of aC2GnT3 polypeptide including substances that interfere with or enhancethe expression or activity of a C2GnT3 polypeptide.

[0106] Substances and compounds identified using the methods of theinvention include but are not limited to peptides such as solublepeptides including Ig-tailed fusion peptides, members of random peptidelibraries and combinatorial chemistry-derived molecular libraries madeof D-and/or L-configuration amino acids, phosphopeptides (includingmembers of random or partially degenerate, directed phosphopeptidelibraries), antibodies [e.g. polyclonal, monoclonal, humanized,anti-idiotypic, chimeric, single chain antibodies, fragments, (e.g. Fab,F(ab)₂, and Fab expression library fragments, and epitope-bindingfragments thereof)], polypeptides, nucleic acids, carbohydrates, andsmall organic or inorganic molecules. A substance or compound may be anendogenous physiological compound or it may be a natural or syntheticcompound.

[0107] Modulation of a C2GnT3 polypeptide can be evaluated, forinstance, by evaluating the inhibitory/stimulatory effect of an agent onC2GnT3 biological activity in comparison to a control or reference. Thecontrol or reference may be, e.g., a predetermined reference value, ormay be evaluated experimentally. For example, in a cell-based assaywhere a host cell expressing recombinant C2GnT3 is incubated in a mediumcontaining a potential modulating agent, a control or reference may be,e.g., a host cell incubated with an agent having a known effect onC2GnT3 expression/activity, a host cell incubated in the same mediumwithout any agent, a host cell transfected with a “mock” vector notexpressing any C2GnT3 polypeptide, or any other suitable control orreference. In a cell-free assay where C2GnT3 polypeptide is incubated ina medium containing a potential modulating agent, a control or referencemay be, for example, medium not containing C2GnT3 polypeptide, mediumnot containing any agent, medium containing a reference polypeptide oragent, or any other suitable control or reference.

[0108] Substances which modulate a C2GnT3 polypeptide can be identifiedbased on their ability to associate with a C2GnT3 polypeptide.Therefore, the invention also provides methods for identifyingsubstances that associate with a C2GnT3 polypeptide. Substancesidentified using the methods of the invention may be isolated, clonedand sequenced using conventional techniques. A substance that associateswith a polypeptide of the invention may be an agonist or antagonist ofthe biological or immunological activity of a polypeptide of theinvention.

[0109] The term “agonist” refers to a molecule that increases the amountof, or prolongs the duration of, the activity of the polypeptide. Theterm “antagonist” refers to a molecule which decreases the biological orimmunological activity of the polypeptide. Agonists and antagonists mayinclude proteins, nucleic acids, carbohydrates, or any other moleculesthat associate with a polypeptide of the invention.

[0110] Substances which can associate with a C2GnT3 polypeptide may beidentified by reacting a C2GnT3 polypeptide with a test substance whichpotentially associates with a C2GnT3 polypeptide, under conditions whichpermit the association, and removing and/or detecting the associatedC2GnT3 polypeptide and substance. Substance-polypeptide complexes, freesubstance, or non-complexed polypeptides may be assayed. Conditionswhich permit the formation of substance-polypeptide complexes may beselected having regard to factors such as the nature and amounts of thesubstance and the polypeptide.

[0111] The substance-polypeptide complex, free substance ornon-complexes polypeptides may be isolated by conventional isolationtechniques, for example, salting out, chromatography, electrophoresis,gel filtration, fractionation, absorption, polyacrylamide gelelectrophoresis, agglutination, or combinations thereof. To facilitatethe assay of the components, antibody against a polypeptide of theinvention or the substance, or labelled polypeptide, or a labelledsubstance may be utilized. The antibodies, polypeptides, or substancesmay be labelled with a detectable substance as described above.

[0112] A C2GnT3 polypeptide, or the substance used in the method of theinvention may be insolubilized. For example, a polypeptide, or substancemay be bound to a suitable carrier such as agarose, cellulose, dextran,Sephadex, Sepharose, carboxymethyl cellulose polystyrene, filter paper,ion-exchange resin, plastic film, plastic tube, glass beads,polyamine-methyl vinyl-ether-maleic acid copolymer, amino acidcopolymer, ethylene-maleic acid copolymer, nylon, silk, etc. The carriermay be in the shape of, for example, a tube, test plate, beads, disc,sphere etc. The insolubilized polypeptide or substance may be preparedby reacting the material with a suitable insoluble carrier using knownchemical or physical methods, for example, cyanogen bromide coupling.

[0113] The invention also contemplates a method for evaluating acompound for its ability to modulate the biological activity of apolypeptide of the invention, by assaying for an agonist or antagonist(i.e. enhancer or inhibitor) of the association of the polypeptide witha substance which interacts with the polypeptide (e.g. donor or acceptorsubstrates or parts thereof). The basic method for evaluating if acompound is an agonist or antagonist of the association of a polypeptideof the invention and a substance that associates with the polypeptide isto prepare a reaction mixture containing the polypeptide and thesubstance under conditions which permit the formation ofsubstance-polypeptide complexes, in the presence of a test compound. Thetest compound may be initially added to the mixture, or may be addedsubsequent to the addition of the polypeptide and substance. Controlreaction mixtures without the test compound or with a placebo are alsoprepared. The formation of complexes is detected and the formation ofcomplexes in the control reaction but not in the reaction mixtureindicates that the test compound interferes with the interaction of thepolypeptide and substance. The reactions may be carried out in theliquid phase or the polypeptide, substance, or test compound may beimmobilized as described herein. The agent can be selected fromcompounds, compositions, antibodies or antibody fragments, antisensesequences and ribozyme nucleotide sequences for C2GnT3 polypeptide.

[0114] It will be understood that the agonists and antagonists i.e.inhibitors and enhancers, that can be assayed using the methods of theinvention may act on one or more of the interaction sites an thepolypeptide or substance including agonist binding sites, competitiveantagonist binding cites, non-competitive antagonist binding sites orallosteric sites.

[0115] The invention also makes it possible to screen for antagoniststhat inhibit the effects of an agonist of the interaction of apolypeptide of the invention with a substance which is capable ofassociating with the polypeptide. Thus, the invention may be used toassay for a compound that competes for the same interacting site of apolypeptide of the invention.

[0116] Substances that modulate a C2GnT3 polypeptide of the inventioncan be identified based on their ability to interfere with or enhancethe activity of a C2GnT3 polypeptide. Therefore, the invention providesa method for evaluating a compound for its ability to modulate theactivity of a C2GnT3 polypeptide comprising (a) reacting an acceptorsubstrate and a donor substrate for a C2GnT3 polypeptide in the presenceof a test substance; (b) measuring the amount of donor substratetransferred to acceptor substrate, and (c) carrying out steps (a) and(b) in the absence of the test substance to determine if the substanceinterferes with or enhances transfer of the sugar donor to the acceptorby the C2GnT3 polypeptide.

[0117] Suitable acceptor substrate for use in the methods of theinvention are a saccharide, oligosaccharides, polysaccharides,polypeptides, glycopolypeptides, or glycolipids which are eithersynthetic with linkers at the reducing end or naturally occuringstructures, for example, asialo-agalacto-fetuin glycopeptide. Acceptorswill generally comprise β-D-galactosyl-1,3-N-acetyl-D-galactosaminyl-.

[0118] The donor substrate may be a nucleotide sugar,dolichol-phosphate-sugar or dolichol-pyrophosphate-oligosaccharide, forexample, uridine diphospho-N-acetylglucosarnine (UDP-GlcNAc), orderivatives or analogs thereof. The C2GnT3 polypeptide may be obtainedfrom natural sources or produced used recombinant methods as describedherein.

[0119] The acceptor or donor substrates may be labeled with a detectablesubstance as described herein, and the interaction of the polypeptide ofthe invention with the acceptor and donor will give rise to a detectablechange. The detectable change may be calorimetric, photometric,radiometric, potentiometric, etc. The activity of C2GnT3 polypeptide ofthe invention may also be determined using methods based on HPLC(Koenderman et al., FEBS Lett. 222: 42, 1987) or methods employedsynthetic oligosaccharide acceptors attached to hydrophobic aglycones(Palcic et al Glycoconjugate 5:49, 1988; and Pierce et al, Biochem.Biophys. Res. Comm. 146: 679, 1987).

[0120] The C2GnT3 polypeptide is reacted with the acceptor and donorsubstrates at a pH and temperature effective for the polypeptide totransfer the donor to the acceptor, and where one of the components islabeled, to produce a detectable change. It is preferred to use a bufferwith the acceptor and donor to maintain the pH within the pH rangeeffective for the polypeptides. The buffer, acceptor and donor may beused as an assay composition. Other compounds such as EDTA anddetergents may be added to the assay composition.

[0121] The reagents suitable for applying the methods of the inventionto evaluate compounds that modulate a C2GnT3 polypeptide may be packagedinto convenient kits providing the necessary materials packaged intosuitable containers. The kits may also include suitable supports usefulin performing the methods of the invention.

[0122] Substances that modulate a C2GnT3 polypeptide can also beidentified by treating immortalized cells which express the polypeptidewith a test substance, and comparing the morphology of the cells withthe morphology of the cells in the absence of the substance and/or withimmortalized cells which do not express the polypeptide. Examples ofimmortalized cells that can be used include lung epithelial cell linessuch as MvlLu or HEK293 (human embryonal kidney) transfected with avector containing a nucleic acid of the invention. In the absence of aninhibitor the cells show signs of morphologic transformation (e.g.fibroblastic morphology, spindle shape and pile up; the cells are lessadhesive to substratum; there is less cell to cell contact in monolayerculture; there is reduced growth-factor requirements for survival andproliferation; the cells grow in soft-agar of other semi-solid medium;there is a lack of contact inhibition and increased apoptosis inlow-serum high density cultures; there is enhanced cell motility, andthere is invasion into extracellular matrix and secretion of proteases).Substances that inhibit one or more phenotypes may be considered aninhibitor.

[0123] A substance that inhibits a C2GnT3 polypeptide may be identifiedby treating a cell which expresses the polypeptide with a testsubstance, and assaying for complex core 2-based O-linked structures(e.g. repeating Gal[β]1-4GlcNAc[β]) associated with the cell. Thecomplex core 2-based O-linked structures can be assayed using a.substance that binds to the structures (e.g. antibodies). Cells thathave not been treated with the substance or which do not express thepolypeptide may be employed as controls.

[0124] Substances which inhibit transcription or translation of a C2GnT3gene may be identified by transfecting a cell with an expression vectorcomprising a recombinant molecule of the invention, including a reportergene, in the presence of a test substance and comparing the level ofexpression of the C2GnT3 polypeptide, or the expression of thepolypeptide encoded by the reporter gene with a control cell transfectedwith the nucleic acid molecule in the absence of the substance. Themethod can be used to identify transcription and translation inhibitorsof a C2GnT3 gene.

Compositions and Treatments

[0125] The substances or compounds identified by the methods describedherein, polypeptides, nucleic acid molecules, and antibodies of theinvention may be used for modulating the biological activity of a C2GnT3polypeptide, and they may be used in the treatment of conditionsmediated by a C2GnT3 polypeptide. In particular, they may be used toT-cell development and lymphocyte homing and they may be used in theprevention and treatment of thymus-related disorders.

[0126] Therefore, the present invention may be useful for diagnosis ortreatment of various thymus-related disorders in mammals, preferablyhumans. Such disorders include the following: tumors and cancers,hypoactivity, hyperactivity, atrophy, enlargement of the thymus, and thelike. Other disorders include disregulation of T-lymphocyte selection oractivity and would include but not be limited to disorders involvingautoimmunity, arthritis, leukemias, lymphomas, immunosuppression,sepsis, wound healing, acute and chronic in action, cell mediatedimmunity, humor immunity, TH1/TH2 imbalance, and the like.

[0127] The substances or compounds identified by the methods describedherein, antibodies, and polypeptides, and nucleic acid molecules of theinvention may be useful in the prevention and treatment of tumors. Tumormetastasis may be inhibited or prevented by inhibiting the adhesion ofcirculating cancer cells. The substances, compounds, etc. of theinvention may be especially useful in the treatment of various forms ofneoplasia such as leukemias, lymphomas, melanomas, adenomas, sarcomas,and carcinomas of solid tissues in patients. In particular thecomposition may be used for treating malignant melanoma, pancreaticcancer, cervico-uterine cancer, cancer of the liver, kidney, stomach,lung, rectum, breast, bowel, gastric, thyroid, neck, cervix, salivarygland, bile duct, pelvis, mediastinum, urethra, bronchogenic, bladder,esophagus and colon, and Kaposi's Sarcoma which is a form of cancerassociated with HIV-infected patients with Acquired Immune DeficiencySyndrome (AIDS). The substances etc. are particularly useful in theprevention and treatment of tumors of the immune system and thymus andthe metastases derived from these tumors.

[0128] A substance or compound identified in accordance with the methodsdescribed herein, antibodies, polypeptides, or nucleic acid molecules ofthe invention may be used to modulate T-cell activation andimmunodeficiency due to the Wiskott-Aldrich syndrome or AIDS, or tostimulate hematopoietic progenitor cell growth, and/or confer protectionagainst chemotherapy and radiation therapy in a subject.

[0129] Accordingly, the substances, antibodies, and compounds may beformulated into pharmaceutical compositions for administration tosubjects in a biologically compatible form suitable for administrationin vivo. By biologically compatible form suitable for administration invivo is meant a form of the substance to be administered in which anytoxic effects are outweighed by the therapeutic effects. The substancesmay be administered to living organisms including humans, and animals.Administration of a therapeutically active amount of the pharmaceuticalcompositions of the present invention is defined as an amount effective,at dosages and for periods of time necessary to achieve the desiredresult. For example, a therapeutically active amount of a substance mayvary according to factors such as the disease state, age, sex, andweight of the individual, and the ability of antibody to elicit adesired response in the individual. Dosage regima may be adjusted toprovide the optimum therapeutic response. For example, several divideddoses may be administeted daily or the dose may be proportionallyreduced as indicated by the exigencies of the therapeutic situation.

[0130] The active substance may be administered in a convenient mannersuch as by injection (subcutaneous, intravenous, etc.), oraladministration, inhalation, transdermal application, or rectaladministration. Depending on the route of administration, the activesubstance may be coated in a material to protect the compound from theaction of enzymes, acids and other natural conditions that mayinactivate the compound.

[0131] The compositions described herein can be prepared by methodsknown per se for the preparation of pharmaceutically acceptablecompositions which can be administered to subjects, such that aneffective quantity of the active substance is combined in a mixture witha pharmaceutically acceptable vehicle. Suitable vehicles are described,for example, in Remington's Pharmaceutical Sciences (Remington'sPharmaceutical Sciences, Mack Publishing Company, Easton, Pa., USA1985). On this basis, the compositions include, albeit not exclusively,solutions of the substances or compounds in association with one or morepharmaceutically acceptable vehicles or diluents, and contained inbuffered solutions with a suitable pH and iso-osmotic with thephysiological fluids.

[0132] After pharmaceutical compositions have been prepared, they can beplaced in an appropriate container and labeled for treatment of anindicated condition. For administration of an inhibitor of a polypeptideof the invention, such labeling would include amount, frequency, andmethod of administration.

[0133] The nucleic acids encoding C2GnT3 polypeptides or any fragmentthereof, or antisense sequences may be used for therapeutic purposes.Antisense to a nucleic acid molecule encoding a polypeptide of theinvention may be med in situations to block the synthesis of thepolypeptide. In particular, cells may be transformed with sequencescomplementary to nucleic acid molecules encoding C2GnT3 polypeptide.Thus, antisense sequences may be used to modulate C2GnT3 activity or toachieve regulation of gene function. Sense or antisense oligomers orlarger fragments, can be designed from various locations along thecoding or regulatory regions of sequences encoding a polypeptide of theinvention.

[0134] Expression vectors may be derived from retroviruses,adenoviruses, herpes or vaccinia viruses or from various bacterialplasmids for delivery of nucleic acid sequences to the target organ,tissue, or cells. Vectors that express antisense nucleic acid sequencesof C2GnT3 polypeptide can be constructed using techniques well known tothose skilled in the art (see for example, Sambrook, Fritsch, Maniatis,Molecular Cloning, A Laboratory Manual, Second Edition (1989) ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

[0135] Genes encoding C2CnT3 polypeptide can be turned off bytransforming a cell or tissue with expression vectors that express highlevels of a nucleic acid molecule or fragment thereof which encodes apolypeptide of the invention. Such constructs may be used to introduceuntranslatable sense or antisense sequences into a cell. Even if they donot integrate into the DNA, the vectors may continue to transcribe RNAmolecules until all copies are disabled by endogenous nucleases.Transient expression may last for extended periods of time (e.g. a monthor more) with a non-replicating vector or if appropriate replicationelements are part of the vector system.

[0136] Modification of gene expression may be achieved by designingantisense molecules, DNA, RNA, or PNA, to the control regions of aC2GnT3 polypeptide gene i.e. the promoters, enhancers, and introns.Preferably the antisense molecules are oligonucleotides derived from thetranscription initiation site (e.g. between positions −10 and +10 fromthe start site). Inhibition can also be achieved by using triple-helixbase-pairing techniques. Triple helix pairing causes inhibition of theability of the double helix to open sufficiently for the binding ofpolymerases, transcription factors, or regulatory molecules (see Gee J.E. et al (1994) In: Huber, B. E. and B. I. Carr, Molecular andImmunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y.).

[0137] Ribozymes, enzymatic RNA molecules, may be used to catalyze thespecific cleavage of RNA. Ribozyme action involves sequence-specifichybridization of the ribozyme molecule to complementary target RNA,followed by endonucleolytic cleavage. For example, hammerhead motifribozyme molecules may be engineered that can specifically andefficiently catalyze endonucleolytic cleavage of sequences encoding apolypeptide of the invention.

[0138] Specific ribosome cleavage sites within any RNA target may beinitially identified by scanning the target molecule for ribozymecleavage sites which include the following sequences: GUA, GUU, and GUC.Short RNA sequences of between 15 and 20 ribonucleotides correspondingto the region of the cleavage site of the target gene may be evaluatedfor secondary structural features which may render the oligonucleotideinoperable. The suitability of candidate targets may be evaluated bytesting accessibility to hybridization with complementaryoligonucleotides using ribonuclease protection assays.

[0139] Therapeutic efficacy and toxicity may be determined by standardpharmaceutical procedures in cell cultures or with experimental animals,such as by calculating the ED₅₀ (the dose therapeutically effective in50% of the population) or LD₅₀ (the dose lethal to 50% of thepopulation) statistics. The therapeutic index is the dose ratio oftherapeutic to toxic effects and it can be expressed as the ED₅₀/LD₅₀ratio. Pharmaceutical compositions which exhibit large therapeuticindices are preferred.

[0140] The invention also provides methods for studying the function ofa C2GnT3 polypeptide. Cells, tissues, and non-human animals lacking inC2GnT3 expression or partially lacking in C2GnT3 expression may bedeveloped using recombinant expression vectors of the invention havingspecific deletion or insertion mutations in a C2GnT3 gene. A recombinantexpression vector may be used to inactivate or alter the endogenous geneby homologous recombination, and thereby create a C2GnT3 deficient cell,tissue or animal.

[0141] Null alleles may be generated in cells, such as embryonic stemcells by deletion mutation. A recombinant C2GnT3 gene may also beengineered to contain an insertion mutation which inactivates C2GnT3.Such a construct may then be introduced into a cell, such as anembryonic stem cell, by a technique such as transfection,elcctroporation, injection etc. Cells lacking an intact C2GnT3 gene maythen be identified, for example by Southern blotting, Northern Blottingor by assaying for expression of a polypeptide of the invention usingthe methods described herein. Such cells may then be used to generatetransgenic non-human animals deficient in C2GnT3. Germline transmissionof the mutation may be achieved, for example, by aggregating theembryonic stem cells with early stage embryos, such as 8 cell embryos,in vitro; transferring the resulting blastocysts into recipient femalesand; generating germline transmission of the resulting aggregationchimeras. Such a mutant animal may be used to define specific cellpopulations, developmental patterns and in vivo processes, normallydependent on C2GnT3 expression.

[0142] The invention thus provides a transgenic non-human mammal all ofwhose germ cells and somatic cells contain a recombinant expressionvector that inactivates or alters a gene encoding a C2GnT3 polypeptide.Further the invention provides a transgenic non-human mammal, which doesnot express a C2GnT3 polypeptide of the invention.

[0143] A transgenic non-human animal includes but is not limited tomouse, rat, rabbit, sheep, hamster, guinea pig, micro-pig, pig, dog,cat, goat, and non-human primate, preferably mouse.

[0144] The invention also provides a transgenic non-human animal assaysystem which provides a model system for testing for an agent thatreduces or inhibits a pathology associated with a C2GnT3 polypeptidecomprising: (a) administering the agent to a transgenic non-human animalof the invention; and (b) determining whether said agent reduces orinhibits the pathology in the transgenic non-human animal relative to atransgenic non-human animal of step (a) to which the agent has not beenadministered.

[0145] The agent may be useful to treat the disorders and conditionsdiscussed herein. The agents may also be incorporated in apharmaceutical composition as described herein.

[0146] A polypeptide of the invention may be used to support thesurvival, growth, migration, and/or differentiation of cells expressingthe polypeptide. Thus, a polypeptide of the invention may be used as asupplement to support, for example cells in culture.

Methods to Prepare Oligosaccharides

[0147] The invention relates to a method for preparing anoligosaccharide comprising contacting a reaction mixture comprising anactivated donor substrate e.g. GlcNAc, and an acceptor substrate in thepresence of a polypeptide of the invention.

[0148] Examples of acceptor substrates for use in the method forpreparing an oligosaccharide are a saccharide, oligosaccharides,polysaccharides, glycopeptides, glycopolypeptides, or glycolipids whichare either synthetic with linkers at the reducing end or naturallyoccurring structures, for example, asialo-agalacto-fetuin glycopeptide.The activated donor substrate is preferably GlcNAc which may be part ofa nucleotide-sugar, a dolichol-phosphate-sugar, ordolichol-pyrophosphate-oligosaccharide.

[0149] In an embodiment of the invention, the oligosaccharides areprepared on a carrier that is non-toxic to a mammal, in particular ahuman such as a lipid isoprenoid or polyisoprenoid alcohol. An exampleof a suitable carrier is dolichol phosphate. The oligosaccharide may beattached to a carrier via a labile bond allowing for chemical removal ofthe oligosaccharide from the lipid carrier. In the alternative, theoligosaccharide transferase may be used to transfer the oligosaccharidefrom a lipid carrier to a polypeptide.

[0150] The following examples are intended to further illustrate theinvention without limiting its scope.

EXAMPLE 1 A: Identification of cDNA Homologous to C2GnT3 by Analysis ofGSS Database Sequence Information.

[0151] Database searches were performed with the coding sequence of thehuman C2/4GnT (C2GnT2) sequence using the BLASTn and tBLASTn algorithmsagainst the GSS database at The National Center for BiotechnologyInformation, USA. The BLASTn algorithm was used to identify GSSsrepresenting the query gene (identities of ≧95%), whereas tBLASTn wasused to identify non-identical, but similar GSS sequences. GSSs with50-90% nucleotide sequence identity were regarded as different from thequery sequence. Composites of the sequence information for two GSSs werecompiled and analysed for sequence similarity to human C2/4GnT (C2GnT2).

B: Cloning and Sequencing of C2GnT3

[0152] A GSS clone CIT-HSP-2288B17.TF (GSS GenBank accession numberAQ005888), derived from a putative homologue to C2/4GnT (C2GnT2), wasobtained from Research Genetics Inc., USA. Sequencing of this clonerevealed a partial open reading frame with significant sequencesimilarity to C2/4GnT (C2GnT2). The coding region of human C2GnT-L(C2GnT1), C2/4GnT (C2GnT2) and a bovine homologue was previously foundto be organized in one exon ((22),(15)). Since the 3′ sequence availablefrom the C2GnT3 GSS was incomplete but likely to be located in thesingle exon, the missing 3′ portion of the open reading frame wasobtained by sequencing a genomic P1 clone. The P1 clone was obtainedfrom a human foreskin genomic P1 library (DuPont Merck PharmaceuticalCo. Human Foreskin Fibroblast P1 Library) by screening with the primerpair: TSHC96 (5′-GGTTTCACCGTCTCCAACATA-3′, SEQ ID NO:3) and TSHC101(5′-TCGTAAGGCACCTGATACTT-3′, SEQ ID NO:6).

[0153] One genomic clone for C2GnT3, GS22597 #844/B1 was obtained fromGenome Systems Inc., USA. DNA from P1 phage was prepared as recommendedby Genome Systems Inc. The entire coding sequence of the C2GnT3 gene wasrepresented in the clone and sequenced in full using automatedsequencing (ABI377, Perkin-Elmer). Confirmatory sequencing was performedon a cDNA clone obtained by PCR (30 cycles at 95° C. for 10 sec; 55° C.for 15 sec and 68° C. for 2 min 30 sec) on cDNA from human thymus polyA-mRNA with the sense primer: TSHC99(5′-CGAGGATCCAGAATGAAGATATTCAAATGTTA-3′, SEQ ID NO:4), and theanti-sense primer: TSHC121 (5′-AGCGAATTCTTACTATCATGATGTGGTAGTG-3′, SEQID NO: 9).

[0154] The composite sequence contained an open reading frame of 1359base pairs encoding a putative protein of 453 amino acids with type IIdomain structure predicted by the TMpred-algorithm at the SwissInstitute for Experimental Cancer Research(ISREC).(http://www.ch.embnet.org/software/TMPRED_form.html).

EXAMPLE 2 A: Expresson of C2GnT3 in Sf9 Cells

[0155] An expression vector construct designed to encode amino acidresidues 39-453 of C2GnT3 was prepared by PCR using P1 DNA, and theprimer pair: TSHC100 (5′-CGAGGATCCGCAAAAAGACATTTACTTGGTT-3′, SEQ IDNO:5) and TSHC121 (5′-AGCGAATTCTTACTATCATGATGTGGTAGTG-3′, SEQ ID NO:9)

[0156] with BamH1 and EcoRI restriction sites, respectively (FIG. 2).The PCR product was cloned between the BamHI and EcoRI sites of pAcGP67A(PharMingen), and the insert was fully sequenced. pAcGP67-C2GnT3-sol wasco-transfected with Baculo-Gold™ DNA (PharMingen) as describedpreviously (23). Recombinant Baculo-viruses were obtained after twosuccessive amplifications in Sf9 cells grown in serum-containing medium,and titers of virus were estimated by titration in 24-well plates withmonitoring of enzyme activities. Transfection of Sf9-cells withpAcGP67-C2GnT3-sol resulted in marked increase in GlcNAc-transferaseactivity compared to uninfected cells or cells infected with a controlconstruct.

B: Analysis of C2GnT3 Activity

[0157] Standard assays were performed using culture supernatant frominfected cells in 50 μl reaction mixtures containing 100 mM MES (pH6.5), 0.1% Nonidet P-40, 150 μM UDP-[ ¹⁴C]-GlcNAc (2,000 cpm/nmol)(Amersham Pharmacia Biotech), and the indicated concentrations ofacceptor substrates (Sigma and Toronto Research Laboratories Ltd., seeTable I for structures). Reaction products were quantified bychromatography on Dowex AG1-×8.

EXAMPLE 3 Restricted Organ Expression Pattern of C2Gn T3

[0158] A human RNA master blot (CLONTECH) was used for expressionanalysis. The cDNA-fragment of soluble C2GnT3 was used as a probe forhybridization. The probe was random primer-labeled using [α³²P]dATP andand the Strip-EZ DNA labeling kit (Ambion). The membrane was probed for6h at 65° C. following the protocol of the manufacturer (CLONTECH) andwashed five times for 20 min each at 65° C. with 2×SSC, 1% SDS and twicefor 20 min each at 55° C. with 0.1×SSC, 0.5% SDS. A human multipletissue Northern blot MTN II (CLONTECH), was probed as described (24),and washed twice for 10 min each at room temperature with 2×SSC, 0.1%SDS; twice for 10 min each at 55° C. with 1×SSC, 0.1% SDS; and once for10 min with 0.1×SSC, 0.1% SDS at 55° C.

EXAMPLE 4 Analysis of C2GnT3 Gene Expression in Peripheral BloodMononuclear Cells

[0159] PCR analysis of C2GnT3 expression in resting and activated humanblood cell fractions was performed using the primer pair: TSHC118(5′-GAGTCAGTGTGGAATTGAATAC-3′, SEQ ID NO:7) and TSHC126(5′-CAACAGTCTCCTCAACCCTG-3′, SEQ ID NO:11).

[0160] PCR amplifications with primers specific for human C2GnT3(C2GnT3) or GAPDH (G3PDH, supplied by the manufacturer) were performedon a normalized human blood cell cDNA panel (MTC from CLONTECH) for 31cycles. Expression of C2GnT3 transcript was detected in all peripheralblood mononuclear cell (PBMC) fractions with particularly high levels ofexpression in CD4 and CD8 positive T-lymphocytes (FIG. 4).

EXAMPLE 5 Analysis of DNA Polymorphism of The C2GnT3 Gene

[0161] Primer pairs such as: TSHC123 (5′-GGGCAGCATTTGCCTAGTATG-3′, SEQID NO:10) and TSHC119 (5′-GATCTCTGATTTGGCTCAGTG-3′, SEQ ID NO:8)

[0162] as described in FIG. 5 have been used for PCR amplification ofindividual sequences of the coding exon. Each PCR product was subclonedand the sequence of 10 clones containing the appropriate insert wasdetermined assuring that both alleles of each individual arecharacterized.

[0163] Polymorphism of the amplified DNA can be analyzed using, e.g.,DNA sequencing, single-strand conformational polymorphism (SSCP) ormismatch mutation.

[0164] From the foregoing it will be evident that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention.

REFERENCES

[0165] 1. Clausen, H. and Bennett, E. P. A family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases control the initiation ofmucin-type O-linked glycosylation. Glycobiology 6: 635-646, 1996.

[0166] 2. Piller, F., Piller, V., Fox, R. I., and Fukuda, M. HumanT-lymphocyte activation is associated with changes in O-glycanbiosynthesis. J. Biol. Chem. 263: 15146-15150, 1988.

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[0168] 4. Yousefi, S., Higgins, E., Daoling, Z., Pollex-Kruger, A.,Hindsgaul, O., and Dennis, J. W. Increased UDP-GlcNAc:Gal beta1-3GalNAc-R (GlcNAc to GalNAc) beta-1, 6-N-acetylglucosaminyltransferaseactivity in metastatic murine tumor cell lines. Control ofpolylactosamine synthesis. J. Biol. Chem. 266: 1772-1782, 1991.

[0169] 5. Fukuda, M. Possible roles of tumor-associated carbohydrateantigens. Cancer Res. 56: 2237-2244, 1996.

[0170] 6. Brockhausen, I., Yang, J. M., Burchell, J., Whitehouse, C.,and Taylor-Papadimitriou, J. Mechanisms underlying aberrantglycosylation of MUC1 mucin in breast cancer cells. Eur. J. Biochem.233: 607-617, 1995.

[0171] 7. Brockhausen, I., Kuhns, W., Schachter, H., Matta, K. L.,Sutherland, D. R., and Baker, M. A. Biosynthesis of O-glycans inleukocytes from normal donors and from patients with leukemia: increasein O-glycan core 2 UDP-GlcNAc:Gal beta 3 GalNAc alpha-R (GlcNAc toGalNAc) beta(1-6)-N-acetylglucosaminyltransferase in leukemic cells.Cancer Res. 51: 1257-1263, 1991.

[0172] 8. Higgins, E. A., Siminovitch, K. A., Zhuang, D. L.,Brockhausen, I., and Dennis, J. W. Aberrant O-linked oligosaccharidebiosynthesis in lymphocytes and platelets from patients with theWiskott-Aldrich syndrome. J. Biol. Chem. 266: 6280-6290, 1991.

[0173] 9. Saitoh, O., Piller, F., Fox, R. I., and Fukuda, M.T-lymphocytic leukemia expresses complex, branched O-linkedoligosaccharides on a major sialoglycoprotein, leukosialin. Blood 77:1491-1499, 1991.

[0174] 10. Springer, G. F. T and Tn, general carcinoma autoantigens.Science 224: 1198-1206, 1984.

[0175] 11. Kumar, R., Camphausen, R. T., Sullivan, F. X., and Cumming,D. A. Core2 beta-1,6-N-acetylglucosaminyltransferase enzyme activity iscritical for P-selectin glycoprotein ligand-1 binding to P-selectin.Blood 88: 3872-3879, 1996.

[0176] 12. Williams, D. and Schachter, H. Mucin synthesis. I. Detectionin canine submaxillary glands of an N- acetylglucosaminyltransferasewhich acts on mucin substrates. J. Biol. Chem. 255: 11247-11252, 1980.

[0177] 13. Bierhuizen, M. F. and Fukuda, M. Expression cloning of a cDNAencoding UDP-GlcNAc:Gal beta 1-3-GalNAc-R (GlcNAc to GalNAc) beta1-6GlcNAc transferase by gene transfer into CHO cells expressing polyomalarge tumor antigen. Proc. Natl. Acad. Sci. U.S.A. 89: 9326-9330, 1992.

[0178] 14. Schwientek, T., Yeh, J. C., Levery, S. B., Keck, B., Merkx,G., van Kessel, A. G., Fukuda, M., and Clausen, H. Control of O-glycanbranch formation. Molecular cloning and characterization of a novelthymus-associated core 2 betal, 6-n-acetylglucosaminyltransferase. J.Biol. Chem. 275: 11106-11113, 2000.

[0179] 15. Schwientek, T., Nomoto, M., Levery, S. B., Merkx, G., vanKessel, A. G., Bennett, E. P., Hollingsworth, M. A., and Clausen, H.Control of O-glycan branch formation. Molecular cloning of human cDNAencoding a novel betal,6-N-acetylglucosaminyltransferase forming core 2and core 4. J. Biol. Chem. 274: 4504-4512, 1999.

[0180] 16. Yeh, J. C., Ong, E., and Fukuda, M. Molecular cloning andexpression of a novel beta-1, 6-N- acetylglucosaminyltransferase thatforms core 2, core 4, and I branches. J. Biol. Chem. 274: 3215-3221,1999.

[0181] 17. Baum, L. G., Pang, M., Perillo, N. L., Wu, T., Delegeane, A.,Uittenbogaart, C. H., Fukuda, M., and Seilhamer, J. J. Human thymicepithelial cells express an endogenous lectin, galectin-1, which bindsto core 2 O-glycans on thymocytes and T lymphoblastoid cells. J. Exp.Med. 181: 877-887, 1995.

[0182] 18. Perillo, N. L., Marcus, M. E., and Baum, L. G. Galectins:versatile modulators of cell adhesion, cell proliferation, and celldeath. J. Mol. Med. 76: 402-412, 1998.

[0183] 19. Perillo, N. L., Pace, K. E., Seilhamer, J. J., and Baum, L.G. Apoptosis of T cells mediated by galectin-1. Nature 378: 736-739,1995.

[0184] 20. Devereux, J., Haeberli, P., and Smithies, O. A comprehensiveset of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395, 1984

[0185] 21. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., andLipman, D. J. Basic local alignment search tool. J. Mol. Biol. 1990,Oct.5., 215: 403-410,

[0186] 22. Bierhuizen, M. F., Maemura, K., Kudo, S., and Fukuda, M.Genomic organization of core 2 and I branching beta-1,6-N-acetylglucosaminyltransferases. Implication for evolution of the beta-1,6-N-acetylglucosaminyltransferase gene family. Glycobiology 5:417-425, 1995.

[0187] 23. Almeida, R., Amado, M., David, L., Levery, S. B., Holmes, E.H., Merkx, G., van Kessel, A. G., Rygaard, E., Hassan, H., Bennett, E.,and Clausen, H. A family of human beta4-galactosyltransferases. Cloningand expression of two novel UDP-galactose: beta-N-acetylglucosaminebetal,4-galactosyltransferases, beta4Gal-T2 and beta4Gal-T3. J. Biol.Chem. 272: 31979-31991, 1997.

[0188] 24. Bennett, E. P., Hassan, H., and Clausen, H. cDNA cloning andexpression of a novel human UDP-N-acetyl-alpha-D- galactosamine.Polypeptide N-acetylgalactosaminyltransferase, GalNAc-T3. J. Biol. Chem.271: 17006-17012, 1996.

[0189] 25. Wandall, H. H., Hassan, H., Mirgorodskaya, E., Kristensen, A.K., Roepstorff, P., Bennett, E. P., Nielsen, P. A., Hollingsworth, M.A., Burchell, J., Taylor-Papadimitriou, J., and Clausen, H. Substratespecificities of three members of the humanUDP-N-acetyl-alpha-D-galactosamine: PolypeptideN-acetylgalactosaminyltransferase family, GalNAc-T1, -T2, and -T3. J.Biol. Chem. 272: 23503-23514, 1997.

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1 17 1 1362 DNA Human 1 atgaagatat tcaaatgtta ttttaaacat accctacagcagaaagtttt catcctgttt 60 ttaaccctat ggctgctctc tttgttaaag cttctaaatgtgagacgact ctttccgcaa 120 aaagacattt acttggttga gtactcccta agtacctcgccttttgtaag aaacagatac 180 actcatgtta aggatgaagt caggtatgaa gttaactgttcgggtatcta tgaacaggag 240 cctttggaaa ttggaaagag tctggaaata agaagaagggacatcattga cttggaggat 300 gatgatgttg tggcaatgac cagtgattgt gacatttatcagactctaag aggttatgct 360 caaaagcttg tctcaaagga ggagaaaagc ttcccaatagcctattcttt ggttgtccac 420 aaagatgcaa ttatggttga aaggcttatc catgctatatacaaccagca caatatttac 480 tgcatccatt atgatcgtaa ggcacctgat accttcaaagttgccatgaa caatttagct 540 aagtgcttct ccaatatttt cattgcttcc aaattagaggctgtggaata tgcccacatt 600 tccagactcc aggctgattt aaattgcttg tcggaccttctgaagtcttc aatccagtgg 660 aaatatgtta tcaacttgtg tgggcaagat tttcccctgaagtcaaattt tgaattggtg 720 tcagagttga aaaaactcaa tggagcaaat atgttggagacggtgaaacc cccaaacagt 780 aaattggaaa gattcactta ccatcatgaa cttagacgggtgccttatga atatgtgaag 840 ctaccaataa ggacaaacat ctccaaggaa gcacccccccataacattca gatatttgtt 900 ggcagtgctt attttgtttt aagtcaagca tttgttaaatatattttcaa caactccatc 960 gttcaagact tttttgcctg gtctaaagac acatactctcctgatgagca cttttgggct 1020 accttgattc gggttccagg aatacctggg gagatttccagatcagccca ggatgtgtct 1080 gatctgcaga gtaagactcg ccttgtcaag tggaattactatgaaggctt tttctatccc 1140 agttgtactg gatctcacct tcgaagcgtg tgtatttatggagctgcaga attaaggtgg 1200 cttatcaaag atggacattg gtttgctaat aaatttgattctaaggtgga ccctatcttg 1260 attaaatgct tggcagaaaa gcttgaagaa cagcagagagactggatcac tttgccctca 1320 gaaaagttat ttatggatag aaatctcact accacatcatga 1362 2 453 PRT Human 2 Met Lys Ile Phe Lys Cys Tyr Phe Lys His ThrLeu Gln Gln Lys Val 1 5 10 15 Phe Ile Leu Phe Leu Thr Leu Trp Leu LeuSer Leu Leu Lys Leu Leu 20 25 30 Asn Val Arg Arg Leu Phe Pro Gln Lys AspIle Tyr Leu Val Glu Tyr 35 40 45 Ser Leu Ser Thr Ser Pro Phe Val Arg AsnArg Tyr Thr His Val Lys 50 55 60 Asp Glu Val Arg Tyr Glu Val Asn Cys SerGly Ile Tyr Glu Gln Glu 65 70 75 80 Pro Leu Glu Ile Gly Lys Ser Leu GluIle Arg Arg Arg Asp Ile Ile 85 90 95 Asp Leu Glu Asp Asp Asp Val Val AlaMet Thr Ser Asp Cys Asp Ile 100 105 110 Tyr Gln Thr Leu Arg Gly Tyr AlaGln Lys Leu Val Ser Lys Glu Glu 115 120 125 Lys Ser Phe Pro Ile Ala TyrSer Leu Val Val His Lys Asp Ala Ile 130 135 140 Met Val Glu Arg Leu IleHis Ala Ile Tyr Asn Gln His Asn Ile Tyr 145 150 155 160 Cys Ile His TyrAsp Arg Lys Ala Pro Asp Thr Phe Lys Val Ala Met 165 170 175 Asn Asn LeuAla Lys Cys Phe Ser Asn Ile Phe Ile Ala Ser Lys Leu 180 185 190 Glu AlaVal Glu Tyr Ala His Ile Ser Arg Leu Gln Ala Asp Leu Asn 195 200 205 CysLeu Ser Asp Leu Leu Lys Ser Ser Ile Gln Trp Lys Tyr Val Ile 210 215 220Asn Leu Cys Gly Gln Asp Phe Pro Leu Lys Ser Asn Phe Glu Leu Val 225 230235 240 Ser Glu Leu Lys Lys Leu Asn Gly Ala Asn Met Leu Glu Thr Val Lys245 250 255 Pro Pro Asn Ser Lys Leu Glu Arg Phe Thr Tyr His His Glu LeuArg 260 265 270 Arg Val Pro Tyr Glu Tyr Val Lys Leu Pro Ile Arg Thr AsnIle Ser 275 280 285 Lys Glu Ala Pro Pro His Asn Ile Gln Ile Phe Val GlySer Ala Tyr 290 295 300 Phe Val Leu Ser Gln Ala Phe Val Lys Tyr Ile PheAsn Asn Ser Ile 305 310 315 320 Val Gln Asp Phe Phe Ala Trp Ser Lys AspThr Tyr Ser Pro Asp Glu 325 330 335 His Phe Trp Ala Thr Leu Ile Arg ValPro Gly Ile Pro Gly Glu Ile 340 345 350 Ser Arg Ser Ala Gln Asp Val SerAsp Leu Gln Ser Lys Thr Arg Leu 355 360 365 Val Lys Trp Asn Tyr Tyr GluGly Phe Phe Tyr Pro Ser Cys Thr Gly 370 375 380 Ser His Leu Arg Ser ValCys Ile Tyr Gly Ala Ala Glu Leu Arg Trp 385 390 395 400 Leu Ile Lys AspGly His Trp Phe Ala Asn Lys Phe Asp Ser Lys Val 405 410 415 Asp Pro IleLeu Ile Lys Cys Leu Ala Glu Lys Leu Glu Glu Gln Gln 420 425 430 Arg AspTrp Ile Thr Leu Pro Ser Glu Lys Leu Phe Met Asp Arg Asn 435 440 445 LeuThr Thr Thr Ser 450 3 21 DNA Artificial Sequence Primer 3 ggtttcaccgtctccaacat a 21 4 32 DNA Artificial Sequence Primer 4 cgaggatccagaatgaagat attcaaatgt ta 32 5 31 DNA Artificial Sequence Primer 5cgaggatccg caaaaagaca tttacttggt t 31 6 20 DNA Artificial SequencePrimer 6 tcgtaaggca cctgatactt 20 7 22 DNA Artificial Sequence Primer 7gagtcagtgt ggaattgaat ac 22 8 21 DNA Artificial Sequence Primer 8gatctctgat ttggctcagt g 21 9 31 DNA Artificial Sequence Primer 9agcgaattct tactatcatg atgtggtagt g 31 10 21 DNA Artificial SequencePrimer 10 gggcagcatt tgcctagtat g 21 11 20 DNA Artificial SequencePrimer 11 caacagtctc ctcaaccctg 20 12 1287 DNA Human 12 atgctgaggacgttgctgcg aaggagactt ttttcttatc ccaccaaata ctactttatg 60 gttcttgttttatccctaat caccttctcc gttttaagga ttcatcaaaa gcctgaattt 120 gtaagtgtcagacacttgga gcttgctggg gagaatccta gtagtgatat taattgcacc 180 aaagttttacagggtgatgt aaatgaaatc caaaaggtaa agcttgagat cctaacagtg 240 aaatttaaaaagcgccctcg gtggacacct gacgactata taaacatgac cagtgactgt 300 tcttctttcatcaagagacg caaatatatt gtagaacccc ttagtaaaga agaggcggag 360 tttccaatagcatattctat agtggttcat cacaagattg aaatgcttga caggctgctg 420 agggccatctatatgcctca gaatttctat tgcgttcatg tggacacaaa atccgaggat 480 tcctatttagctgcagtgat gggcatcgct tcctgtttta gtaatgtctt tgtggccagc 540 cgattggagagtgtggttta tgcatcgtgg agccgggttc aggctgacct caactgcatg 600 aaggatctctatgcaatgag tgcaaactgg aagtacttga taaatctttg tggtatggat 660 tttcccattaaaaccaacct agaaattgtc aggaagctca agttgttaat gggagaaaac 720 aacctggaaacggagaggat gccatcccat aaagaagaaa ggtggaagaa gcggtatgag 780 gtcgttaatggaaagctgac aaacacaggg actgtcaaaa tgcttcctcc actcgaaaca 840 cctctcttttctggcagtgc ctacttcgtg gtcagtaggg agtatgtggg gtatgtacta 900 cagaatgaaaaaatccaaaa gttgatggag tgggcacaag acacatacag ccctgatgag 960 tatctctgggccaccatcca aaggattcct gaagtcccgg gctcactccc tgccagccat 1020 aagtatgatctatctgacat gcaagcagtt gccaggtttg tcaagtggca gtactttgag 1080 ggtgatgtttccaagggtgc tccctacccg ccctgcgatg gagtccatgt gcgctcagtg 1140 tgcattttcggagctggtga cttgaactgg atgctgcgca aacaccactt gtttgccaat 1200 aagtttgacgtggatgttga cctctttgcc atccagtgtt tggatgagca tttgagacac 1260 aaagctttggagacattaaa acactga 1287 13 428 PRT Human 13 Met Leu Arg Thr Leu Leu ArgArg Arg Leu Phe Ser Tyr Pro Thr Lys 1 5 10 15 Tyr Tyr Phe Met Val LeuVal Leu Ser Leu Ile Thr Phe Ser Val Leu 20 25 30 Arg Ile His Gln Lys ProGlu Phe Val Ser Val Arg His Leu Glu Leu 35 40 45 Ala Gly Glu Asn Pro SerSer Asp Ile Asn Cys Thr Lys Val Leu Gln 50 55 60 Gly Asp Val Asn Glu IleGln Lys Val Lys Leu Glu Ile Leu Thr Val 65 70 75 80 Lys Phe Lys Lys ArgPro Arg Trp Thr Pro Asp Asp Tyr Ile Asn Met 85 90 95 Thr Ser Asp Cys SerSer Phe Ile Lys Arg Arg Lys Tyr Ile Val Glu 100 105 110 Pro Leu Ser LysGlu Glu Ala Glu Phe Pro Ile Ala Tyr Ser Ile Val 115 120 125 Val His HisLys Ile Glu Met Leu Asp Arg Leu Leu Arg Ala Ile Tyr 130 135 140 Met ProGln Asn Phe Tyr Cys Val His Val Asp Thr Lys Ser Glu Asp 145 150 155 160Ser Tyr Leu Ala Ala Val Met Gly Ile Ala Ser Cys Phe Ser Asn Val 165 170175 Phe Val Ala Ser Arg Leu Glu Ser Val Val Tyr Ala Ser Trp Ser Arg 180185 190 Val Gln Ala Asp Leu Asn Cys Met Lys Asp Leu Tyr Ala Met Ser Ala195 200 205 Asn Trp Lys Tyr Leu Ile Asn Leu Cys Gly Met Asp Phe Pro IleLys 210 215 220 Thr Asn Leu Glu Ile Val Arg Lys Leu Lys Leu Leu Met GlyGlu Asn 225 230 235 240 Asn Leu Glu Thr Glu Arg Met Pro Ser His Lys GluGlu Arg Trp Lys 245 250 255 Lys Arg Tyr Glu Val Val Asn Gly Lys Leu ThrAsn Thr Gly Thr Val 260 265 270 Lys Met Leu Pro Pro Leu Glu Thr Pro LeuPhe Ser Gly Ser Ala Tyr 275 280 285 Phe Val Val Ser Arg Glu Tyr Val GlyTyr Val Leu Gln Asn Glu Lys 290 295 300 Ile Gln Lys Leu Met Glu Trp AlaGln Asp Thr Tyr Ser Pro Asp Glu 305 310 315 320 Tyr Leu Trp Ala Thr IleGln Arg Ile Pro Glu Val Pro Gly Ser Leu 325 330 335 Pro Ala Ser His LysTyr Asp Leu Ser Asp Met Gln Ala Val Ala Arg 340 345 350 Phe Val Lys TrpGln Tyr Phe Glu Gly Asp Val Ser Lys Gly Ala Pro 355 360 365 Tyr Pro ProCys Asp Gly Val His Val Arg Ser Val Cys Ile Phe Gly 370 375 380 Ala GlyAsp Leu Asn Trp Met Leu Arg Lys His His Leu Phe Ala Asn 385 390 395 400Lys Phe Asp Val Asp Val Asp Leu Phe Ala Ile Gln Cys Leu Asp Glu 405 410415 His Leu Arg His Lys Ala Leu Glu Thr Leu Lys His 420 425 14 1317 DNAHuman 14 atggttcaat ggaagagact ctgccagctg cattacttgt gggctctgggctgctatatg 60 ctgctggcca ctgtggctct gaaactttct ttcaggttga agtgtgactctgaccacttg 120 ggtctggagt ccagggaatc tcaaagccag tactgtagga atatcttgtataatttcctg 180 aaacttccag caaagaggtc tatcaactgt tcaggggtca cccgaggggaccaagaggca 240 gtgcttcagg ctattctgaa taacctggag gtcaagaaga agcgagagcctttcacagac 300 acccactacc tctccctcac cagagactgt gagcacttca aggctgaaaggaagttcata 360 cagttcccac tgagcaaaga agaggtggag ttccctattg catactctatggtgattcat 420 gagaagattg aaaactttga aaggctactg cgagctgtgt atgcccctcagaacatatac 480 tgtgtccatg tggatgagaa gtccccagaa actttcaaag aggcggtcaaagcaattatt 540 tcttgcttcc caaatgtctt catagccagt aagctggttc gggtggtttatgcctcctgg 600 tccagggtgc aagctgacct caactgcatg gaagacttgc tccagagctcagtgccgtgg 660 aaatacttcc tgaatacatg tgggacggac tttcctataa agagcaatgcagagatggtc 720 caggctctca agatgttgaa tgggaggaat agcatggagt cagaggtacctcctaagcac 780 aaagaaaccc gctggaaata tcactttgag gtagtgagag acacattacacctaaccaac 840 aagaagaagg atcctccccc ttataattta actatgttta cagggaatgcgtacattgtg 900 gcttcccgag atttcgtcca acatgttttg aagaacccta aatcccaacaactgattgaa 960 tgggtaaaag acacttatag cccagatgaa cacctctggg ccacccttcagcgtgcacgg 1020 tggatgcctg gctctgttcc caaccacccc aagtacgaca tctcagacatgacttctatt 1080 gccaggctgg tcaagtggca gggtcatgag ggagacatcg ataagggtgctccttatgct 1140 ccctgctctg gaatccacca gcgggctatc tgcgtttatg gggctggggacttgaattgg 1200 atgcttcaaa accatcacct gttggccaac aagtttgacc caaaggtagatgataatgct 1260 cttcagtgct tagaagaata cctacgttat aaggccatct atgggactgaactttga 1317 15 438 PRT Human 15 Met Val Gln Trp Lys Arg Leu Cys Gln LeuHis Tyr Leu Trp Ala Leu 1 5 10 15 Gly Cys Tyr Met Leu Leu Ala Thr ValAla Leu Lys Leu Ser Phe Arg 20 25 30 Leu Lys Cys Asp Ser Asp His Leu GlyLeu Glu Ser Arg Glu Ser Gln 35 40 45 Ser Gln Tyr Cys Arg Asn Ile Leu TyrAsn Phe Leu Lys Leu Pro Ala 50 55 60 Lys Arg Ser Ile Asn Cys Ser Gly ValThr Arg Gly Asp Gln Glu Ala 65 70 75 80 Val Leu Gln Ala Ile Leu Asn AsnLeu Glu Val Lys Lys Lys Arg Glu 85 90 95 Pro Phe Thr Asp Thr His Tyr LeuSer Leu Thr Arg Asp Cys Glu His 100 105 110 Phe Lys Ala Glu Arg Lys PheIle Gln Phe Pro Leu Ser Lys Glu Glu 115 120 125 Val Glu Phe Pro Ile AlaTyr Ser Met Val Ile His Glu Lys Ile Glu 130 135 140 Asn Phe Glu Arg LeuLeu Arg Ala Val Tyr Ala Pro Gln Asn Ile Tyr 145 150 155 160 Cys Val HisVal Asp Glu Lys Ser Pro Glu Thr Phe Lys Glu Ala Val 165 170 175 Lys AlaIle Ile Ser Cys Phe Pro Asn Val Phe Ile Ala Ser Lys Leu 180 185 190 ValArg Val Val Tyr Ala Ser Trp Ser Arg Val Gln Ala Asp Leu Asn 195 200 205Cys Met Glu Asp Leu Leu Gln Ser Ser Val Pro Trp Lys Tyr Phe Leu 210 215220 Asn Thr Cys Gly Thr Asp Phe Pro Ile Lys Ser Asn Ala Glu Met Val 225230 235 240 Gln Ala Leu Lys Met Leu Asn Gly Arg Asn Ser Met Glu Ser GluVal 245 250 255 Pro Pro Lys His Lys Glu Thr Arg Trp Lys Tyr His Phe GluVal Val 260 265 270 Arg Asp Thr Leu His Leu Thr Asn Lys Lys Lys Asp ProPro Pro Tyr 275 280 285 Asn Leu Thr Met Phe Thr Gly Asn Ala Tyr Ile ValAla Ser Arg Asp 290 295 300 Phe Val Gln His Val Leu Lys Asn Pro Lys SerGln Gln Leu Ile Glu 305 310 315 320 Trp Val Lys Asp Thr Tyr Ser Pro AspGlu His Leu Trp Ala Thr Leu 325 330 335 Gln Arg Ala Arg Trp Met Pro GlySer Val Pro Asn His Pro Lys Tyr 340 345 350 Asp Ile Ser Asp Met Thr SerIle Ala Arg Leu Val Lys Trp Gln Gly 355 360 365 His Glu Gly Asp Ile AspLys Gly Ala Pro Tyr Ala Pro Cys Ser Gly 370 375 380 Ile His Gln Arg AlaIle Cys Val Tyr Gly Ala Gly Asp Leu Asn Trp 385 390 395 400 Met Leu GlnAsn His His Leu Leu Ala Asn Lys Phe Asp Pro Lys Val 405 410 415 Asp AspAsn Ala Leu Gln Cys Leu Glu Glu Tyr Leu Arg Tyr Lys Ala 420 425 430 IleTyr Gly Thr Glu Leu 435 16 1203 DNA Human 16 atgcctttat caatgcgttacctcttcata atttctgtct ctagtgtaat tatttttatc 60 gtcttctctg tgttcaattttgggggagat ccaagcttcc aaaggctaaa tatctcagac 120 cctttgaggc tgactcaagtttgcacatct tttatcaatg gaaaaacacg tttcctgtgg 180 aaaaacaaac taatgatccatgagaagtct tcttgcaagg aatacttgac ccagagccac 240 tacatcacag cccctttatctaaggaagaa gctgactttc ccttggcata tataatggtc 300 atccatcatc actttgacacctttgcaagg ctcttcaggg ctatttacat gccccaaaat 360 atctactgtg ttcatgtggatgaaaaagca acaactgaat ttaaagatgc ggtagagcaa 420 ctattaagct gcttcccaaacgcttttctg gcttccaaga tggaacccgt tgtctatgga 480 gggatctcca ggctccaggctgacctgaac tgcatcagag atctttctgc cttcgaggtc 540 tcatggaagt acgttatcaacacctgtggg caagacttcc ccctgaaaac caacaaggaa 600 atagttcagt atctgaaaggatttaaaggt aaaaatatca ccccaggggt gctgccccca 660 gctcatgcaa ttggacggactaaatatgtc caccaagagc acctgggcaa agagctttcc 720 tatgtgataa gaacaacagcgttgaaaccg cctccccccc ataatctcac aatttacttt 780 ggctctgcct atgtggctctatcaagagag tttgccaact ttgttctgca tgacccacgg 840 gctgttgatt tgctccagtggtccaaggac actttcagtc ctgatgagca tttctgggtg 900 acactcaata ggattccaggtgttcctggc tctatgccaa atgcatcctg gactggaaac 960 ctcagagcta taaagtggagtgacatggaa gacagacacg gaggctgcca cggccactat 1020 gtacatggta tttgtatctatggaaacgga gacttaaagt ggctggttaa ttcaccaagc 1080 ctgtttgcta acaagtttgagcttaatacc taccccctta ctgtggaatg cctagaactg 1140 aggcatcgcg aaagaaccctcaatcagagt gaaactgcga tacaacccag ctggtatttt 1200 tga 1203 17 400 PRTHuman 17 Met Pro Leu Ser Met Arg Tyr Leu Phe Ile Ile Ser Val Ser Ser Val1 5 10 15 Ile Ile Phe Ile Val Phe Ser Val Phe Asn Phe Gly Gly Asp ProSer 20 25 30 Phe Gln Arg Leu Asn Ile Ser Asp Pro Leu Arg Leu Thr Gln ValCys 35 40 45 Thr Ser Phe Ile Asn Gly Lys Thr Arg Phe Leu Trp Lys Asn LysLeu 50 55 60 Met Ile His Glu Lys Ser Ser Cys Lys Glu Tyr Leu Thr Gln SerHis 65 70 75 80 Tyr Ile Thr Ala Pro Leu Ser Lys Glu Glu Ala Asp Phe ProLeu Ala 85 90 95 Tyr Ile Met Val Ile His His His Phe Asp Thr Phe Ala ArgLeu Phe 100 105 110 Arg Ala Ile Tyr Met Pro Gln Asn Ile Tyr Cys Val HisVal Asp Glu 115 120 125 Lys Ala Thr Thr Glu Phe Lys Asp Ala Val Glu GlnLeu Leu Ser Cys 130 135 140 Phe Pro Asn Ala Phe Leu Ala Ser Lys Met GluPro Val Val Tyr Gly 145 150 155 160 Gly Ile Ser Arg Leu Gln Ala Asp LeuAsn Cys Ile Arg Asp Leu Ser 165 170 175 Ala Phe Glu Val Ser Trp Lys TyrVal Ile Asn Thr Cys Gly Gln Asp 180 185 190 Phe Pro Leu Lys Thr Asn LysGlu Ile Val Gln Tyr Leu Lys Gly Phe 195 200 205 Lys Gly Lys Asn Ile ThrPro Gly Val Leu Pro Pro Ala His Ala Ile 210 215 220 Gly Arg Thr Lys TyrVal His Gln Glu His Leu Gly Lys Glu Leu Ser 225 230 235 240 Tyr Val IleArg Thr Thr Ala Leu Lys Pro Pro Pro Pro His Asn Leu 245 250 255 Thr IleTyr Phe Gly Ser Ala Tyr Val Ala Leu Ser Arg Glu Phe Ala 260 265 270 AsnPhe Val Leu His Asp Pro Arg Ala Val Asp Leu Leu Gln Trp Ser 275 280 285Lys Asp Thr Phe Ser Pro Asp Glu His Phe Trp Val Thr Leu Asn Arg 290 295300 Ile Pro Gly Val Pro Gly Ser Met Pro Asn Ala Ser Trp Thr Gly Asn 305310 315 320 Leu Arg Ala Ile Lys Trp Ser Asp Met Glu Asp Arg His Gly GlyCys 325 330 335 His Gly His Tyr Val His Gly Ile Cys Ile Tyr Gly Asn GlyAsp Leu 340 345 350 Lys Trp Leu Val Asn Ser Pro Ser Leu Phe Ala Asn LysPhe Glu Leu 355 360 365 Asn Thr Tyr Pro Leu Thr Val Glu Cys Leu Glu LeuArg His Arg Glu 370 375 380 Arg Thr Leu Asn Gln Ser Glu Thr Ala Ile GlnPro Ser Trp Tyr Phe 385 390 395 400

1. An isolated nucleic acid encoding UDP-N-Acetylglucosamine:Galactose-β1,3-N-Acetylgalactosamine-α-R β1-6N-Acetylglucosaminyltransferase (C2GnT3) or a fragment thereof.
 2. Theisolated nucleic acid of claim 1, wherein said nucleic acid is DNA. 3.The isolated nucleic acid of claim 2, wherein said DNA is cDNA.
 4. Theisolated nucleic acid of claim 2, wherein said DNA is genomic DNA. 5.The isolated nucleic acid of claim 1, wherein said isolated nucleic acidcomprises the nucleotide sequence of SEQ ID NO: 1, or asequence-conservative or function-conservative variant thereof.
 6. Anucleic acid which hybridizes under conditions of high stringency with anucleic acid comprising the nucleotide sequence of SEQ ID NO:
 1. 7. Anexpression vector comprising a nucleotide sequence encoding C2GnT3 or afragment thereof.
 8. The vector of claim 7, wherein said nucleotidesequence comprises the nucleotide sequence of SEQ ID NO: 1, or asequence-conservative or function-conservative variant thereof.
 9. Thevector of claim 7, wherein said sequence encoding C2GnT3 is operablylinked to a transcriptional regulatory element.
 10. A cell comprisingthe vector of claim
 7. 11. The cell of claim 10, wherein said cell isstably transfected with said vector.
 12. The cell of claim 10, whereinsaid cell produces enzymatically active C2GnT3.
 13. The cell of claim10, wherein said cell is selected from the group consisting ofbacterial, yeast, insect, avian, and mammalian cells.
 14. The cell inclaim 10, wherein said cell is Sf9.
 15. The cell in claim 10, whereinsaid cell is CHO.
 16. A method for producing C2GnT3 polypeptides, whichmethod comprises: (i) introducing into a host cell an isolated DNAmolecule encoding human C2GnT3, or a DNA construct comprising a DNAsequence encoding C2GnT3; (ii) growing the host cell under conditionssuitable for human C2GnT3 expression; and (iii) isolating C2GnT3produced by the host cell.
 17. The method of claim 16, wherein saidenzymatically active C2GnT3 is selected from the group consisting of:(i) a polypeptide comprising the amino acid sequence of SEQ ID NO: 2;(ii) a polypeptide comprising amino acid residues 39-453 of SEQ ID NO:2; (iii) a polypeptide comprising amino acids residues 39-453 of SEQ IDNO: 2 fused to a second sequence, wherein said second sequence comprisesan affinity ligand or a reactive group; and (iv) a function-conservativevariant of any of the polypeptides in (i) to (iii).
 18. A method ofdetecting whether at least one agent is an inhibitor or stimulator ofC2GnT3 enzymatic activity in a cell-free or cell-based assay, whichmethod comprises: (i) contacting a C2GnT3 polypeptide in claim 17 withsaid at least one agent under assay conditions suitable for thedetection of said enzymatic activity; and (ii) measuring whether saidenzymatic activity is inhibited or stimulated by said at least oneagent, wherein said at least one agent is selected from compounds,compositions, antibodies or antibody fragments, antisense sequences andribozyme nucleotide sequences for C2GnT3 polypeptide.
 19. A method ofdetecting whether at least one agent is an inhibitor or stimulator ofC2GnT3 enzymatic activity in a cell-free or cell-based assay, whichmethod comprises: (i) contacting a cell that recombinantly expressesC2GnT3 polypeptide according to claims 10 with said at least one agentunder assay conditions suitable for the detection of said enzymaticactivity; and (iii) measuring whether said enzymatic activity isinhibited or stimulated by said at least one agent, wherein said atleast one agent is selected from compounds, compositions, antibodies orantibody fragments, antisense sequences and ribozyme nucleotidesequences for C2GnT3 polypeptide.
 20. The method of claim 18, whereinsaid at least one agent is a member of a combinatorial chemical library.21. The method of claim 19, wherein said at least one agent is a memberof a combinatorial chemical library.
 22. The method of claim 18, whereinsaid at least one agent is generated by methods of C2GnT3 polypeptidestructure-based design.
 23. The method of claim 19, wherein said atleast one agent is generated by methods of C2GnT3 polypeptidestructure-based design.
 24. A method for identifying DNA sequencevariations in the C2GnT3 gene, comprising the steps of: (i) isolatingDNA from a patient; (ii) amplifying at least one C2GnT3 genomic regionfrom said DNA by PCR; and (iii) analyzing said amplified C2GnT3 genomicregion by DNA sequencing, single-strand conformational polymorphism(SSCP) or mismatch mutation, to detect whether a sequence variationvis-à-vis SEQ ID NO: 1 exists.
 25. An isolated C2GnT3 polypeptidecomprising the amino acid sequence of SEQ ID NO:
 2. 26. An isolatedpolypeptide having at least 45% amino acid sequence identity to theamino acid sequence of SEQ ID NO:
 2. 27. A polypeptide produced by themethod of claim
 16. 28. An antibody specifically recognizing apolypeptide of any of claims 25 to
 27. 29. A probe comprising a sequenceencoding a polypeptide of any of claims 25 to 27, or a part of apolypeptide of any of claims 25 to
 27. 30. A method of diagnosing ormonitoring conditions mediated by a C2GnT3 polypeptide comprisingdetermining the presence of the nucleic acid molecule of claim 1 in abiological sample.
 31. The method of claim 30, wherein the condition isa thymus-related disorder.
 32. A method of diagnosing or monitoringconditions mediated by a C2GnT3 polypeptide comprising determining thepresence of the nucleic acid molecule of claim 6 in a biological sample.33. The method of claim 32 wherein the condition is a thymus-relateddisorder.
 34. A method of diagnosing or monitoring conditions mediatedby a C2GnT3 polypeptide comprising determining the presence of thenucleic acid molecule of claim 7 in a biological sample.
 35. The methodof claim 34 wherein the condition is a thymus-related disorder.
 36. Amethod of diagnosing or monitoring conditions mediated by a C2GnT3polypeptide comprising determining the presence in a biological sampleof a nucleic acid molecule in claim
 25. 37. The method of claim 36,wherein the condition is a thymus-related disorder.
 38. A method ofdiagnosing or monitoring conditions mediated by a C2GnT3 polypeptidecomprising determining the presence in a biological sample of a nucleicacid molecule in claim
 26. 39. The method of claim 38, wherein thecondition is a thymus-related disorder.
 40. A method of diagnosing ormonitoring conditions mediated by a C2GnT3 polypeptide comprisingdetermining the presence in a biological sample of a nucleic acidmolecule in claim
 27. 41. The method of claim 40, wherein the conditionis a thymus-related disorder.
 42. A method for identifying a substancewhich associates with a polypeptide in any one of claims 22 to 24comprising: (i) reacting the polypeptide with at least one substancewhich potentially can associate with the polypeptide, under conditionswhich permit the association between the substance and polypeptide; and(ii) detecting polypeptide associated with the substance, whereindetection of associated polypeptide and substance indicates that thesubstance associated with the polypeptide.
 43. A method for evaluation acompound for its ability to modulate the biological activity of apolypeptide in any one of claims 25 to 27 comprising providing a knownconcentration of the polypeptide with a substance which associates withthe polypeptide, and a test compound under conditions which permit theformation of complexes between the substance and polypeptide, anddetecting said complexes.
 44. A method for detecting a nucleic acidmolecule encoding a C2GnT3 polypeptide in a biological sample comprisingthe steps of: (i) hybridizing a nucleic acid molecule of claim 1 to thenucleic acid in the biological sample; and (ii) detecting whether ahybridization complex has been formed, wherein the presence of ahybridization complex correlates with the presence of a nucleic acidmolecule encoding the polypeptide in the biological sample.
 45. Themethod in claim 44 wherein nucleic acids of the biological sample areamplified by the polymerase chain reaction prior to the hybridizingstep.
 46. A method for detecting a nucleic acid molecule encoding aC2GnT3 polypeptide in a biological sample comprising the steps of: (i)hybridizing the nucleic acid molecule of claim 6 to the nucleic acid inthe biological sample; and (ii) detecting whether a hybridizationcomplex has been formed, wherein the presence of a hybridization complexcorrelates with the presence of a nucleic acid molecule encoding thepolypeptide in the biological sample.
 47. The method in claim 46 whereinnucleic acids of the biological sample are amplified by the polymerasechain reaction prior to the hybridizing step.
 48. A method for detectinga nucleic acid molecule encoding a C2GnT3 polypeptide in a biologicalsample comprising the steps of: (i) hybridizing the nucleic acidmolecule of claim 7 to the nucleic acid in the biological sample; and(ii) detecting whether a hybridization complex has been formed, whereinthe presence of a hybridization complex correlates with the presence ofa nucleic acid molecule encoding the polypeptide in the biologicalsample.
 49. The method in claim 48 wherein nucleic acids of thebiological sample are amplified by the polymerase chain reaction priorto the hybridizing step.
 50. A method for treating a condition mediatedby a C2GnT3 polypeptide in any one of claims 25 to 27, comprisingadministering an effective amount of the antibody in claim 28, or asubstance or compound identified using a method in any of claims 42 and43.
 51. A method as claimed in claim 50 wherein the condition is athymus-related disorder.
 52. A composition comprising one or more of anucleic acid molecule in any of claims 1, 6, and 7, or the polypeptidein any of claims 25 to 27, or a substance or compound identified using amethod in any of claims 18, 19, 42 and 43, and a pharmaceuticallyacceptable carrier, excipient or diluent.
 53. Use of at least onenucleic acid molecule in any of claims 1, 6, and 7, or the polypeptidein any of claims 25 to 27, or a substance or compound identified using amethod as claimed in any one of claims 18, 19, 42 and 43 in thepreparation of a pharmaceutical composition for treating a conditionmediated by a C2GnT3 polypeptide.
 54. A gene-based therapy directed atthe thymus comprising a polynucleotide comprising all or a portion of aregulatory sequence of SEQ ID NO:
 1. 55. A method for preparing anoligosaccharide comprising contacting a reaction mixture comprising anactivated GlcNAc, and an acceptor in the presence of an enzymaticallyactive polypeptide as claimed in any one of claims 25 to
 27. 56. Anisolated nucleic acid comprising a nucleic acid segment free of internalnon-coding sequences, said segment encoding UDP-N-Acetylglucosamine:Galactose-β1,3-N-Acetyl-galactosamine-α-R β1-6N-Acetylglucosaminyl-transferase (C2GnT3) or a fragment thereof.
 57. Amethod of detecting whether at least one agent is an inhibitor orstimulator of C2GnT3 enzymatic activity, which method comprises: (i)contacting said at least one agent, under assay conditions suitable forthe detection of said enzymatic activity, with a C2GnT3 polypeptideselected from the group consisting of a polypeptide comprising the aminoacid sequence of SEQ ID NO:2; a polypeptide comprising amino acidresidues 39-453 of SEQ ID NO: 2; a polypeptide comprising amino acidsresidues 39-453 of SEQ ID NO: 2 fused to a second sequence, wherein saidsecond sequence comprises an affinity ligand or a reactive group; and afunction-conservative variants of any of the foregoing polypeptides; and(ii) measuring whether said enzymatic activity is inhibited orstimulated compared to a control value by said at least one agent. 58.The method of claim 57, wherein said at least one agent is selected fromthe group consisting of compounds, compositions, antibodies, antibodyfragments, antisense sequences, and ribozyme nucleotide sequences forC2GnT3 polypeptide.
 59. The method of claim 57, wherein said contactingtakes place in a cell-free or a cell-based assay system.
 60. An isolatedpolypeptide having at least 95% amino acid sequence identity to theamino acid sequence of SEQ ID NO: 2, and C2GnT3 enzymatic activity. 61.An antibody specifically recognizing the polypeptide in claim
 60. 62. Anisolated UDP-N-Acetylglucosamine:Galactose-β1,3-N-Acetylgalactosamine-α-R β1,6N-Acetylglucosaminyltransferase (C2GnT) polypeptide comprising the aminoacid sequence of residues 39-453 of SEQ ID NO:
 2. 63. The isolated C2GnTpolypeptide of claim 62, comprising the amino acid sequence of SEQ IDNO:2.
 64. The isolated C2GnT polypeptide of claim 62, having the aminoacid sequence of SEQ ID NO:2.
 65. An isolated C2GnT polypeptide havingat least 45% amino acid sequence identity to the amino acid sequence ofSEQ ID NO:
 2. 66. The isolated C2GnT polypeptide of claim 65, whereinsaid amino acid sequence identity is at least 60%.
 67. The isolatedC2GnT polypeptide of claim 65, wherein said amino acid sequence identityis at least 95%.
 68. An isolated C2GnT polypeptide having at least 45%amino acid sequence identity to a human C2GnT enzyme which is expressedin vivo at a higher level in thymus tissue than in tracheal and thyroidtissue.
 69. The isolated C2GnT polypeptide of claim 68, wherein saidamino acid sequence identity is at least 60%.
 70. The isolated C2GnTpolypeptide of claim 68, wherein said amino acid sequence identity is atleast 95%.
 71. An isolated polypeptide having at least 95% amino acidsequence identity to SEQ ID NO:2 and C2GnT enzymatic activity.
 72. AC2GnT polypeptide produced by a method comprising: (i) introducing intoa host cell an isolated DNA molecule encoding a human C2GnT polypeptide,or a DNA construct comprising a DNA sequence encoding a C2GnTpolypeptide; (ii) growing the host cell under conditions suitable forhuman C2GnT expression; and (iii) isolating C2GnT polypeptide producedby the host cell, wherein said C2GnT polypeptide is at least 45%identical to SEQ ID NO:2.
 73. The C2GnT polypeptide of claim 72, whereinsaid C2GnT polypeptide is at least 60% identical to SEQ ID NO:2.
 74. TheC2GnT polypeptide of claim 72, wherein said C2GnT polypeptide is atleast 95% identical to SEQ ID NO:2.
 75. A method for preparing anoligosaccharide comprising contacting a compound comprising an activatedGlcNAc, an acceptor, and the C2GnT polypeptide of any of claims 62, 65,68, 71, and
 72. 76. A method for preparing an oligosaccharide comprisingcontacting a compound comprising an activated GlcNAc, an acceptor, and aC2GnT polypeptide comprising the amino acid sequence of residues 39-453of SEQ ID NO:
 2. 77. The method of claim 76, wherein the C2GnTpolypeptide comprises the amino acid sequence of SEQ ID NO:2.
 78. Themethod of claim 76, wherein the C2GnT polypeptide has the amino acidsequence of SEQ ID NO:2.
 79. The method of claim 76, wherein saidcompound comprises a nucleotide-sugar, a dolichol-phosphate-sugar, or adolichol-pyrophosphate-oligosaccharide moiety.
 80. The method of claim76, wherein the acceptor is selected from the group consisting of asaccharide, an oligosaccharide, a polysaccharide, a glycopeptide, aglycopolypeptide, and a glycolipid.